The South Korean president's office has called for the already-controversial deployment of the US Army's Terminal High Altitude Area Defense (THAAD) anti-missile system to be suspended in what is being portrayed as an escalating clash between the presidential Blue House and the Ministry of National Defense.

President Moon Jae-in is reported to have been furious after learning that four additional THAAD launchers had been brought into South Korea and were in storage at a US military facility.

Previously, the Blue House said it had been aware of only two launcher units being transferred from the US and deployed at the site of the former Lotte Skyhill Jeju Country Club, in North Gyeongsang Province.

The suggestion in some parts of the South Korean media, which have been encouraged by groups opposed to the deployment of the system in South Korea, is that the military deliberately misled the government on the number of launchers that were in the country.

Full assessment

The Blue House is now demanding a full environmental impact assessment of the THAAD system, a process that could take many months. A similar investigation conducted by the authorities on the Pacific island of Guam took 23 months to complete.

"We are not saying that the two launchers and other equipment that has already been deployed should be withdrawn, but those that have yet to be deployed will have to wait," a senior Blue House official told Yonhap news agency in Seoul.

The need for the most advanced missile defense system available was demonstrated again early on Thursday when North Korea fired a volley of anti-ship cruise missiles from launchers on its east coast. The missiles are estimated to have travelled around 200 kilometers before falling into the Sea of Japan. North Korea has now test-fired missiles on four occasions since Moon was inaugurated in early May.

Read: North Korea crisis: Which country has the strongest military in the region?

The previous South Korean government, of President Park Geun-hye, approved the installation of the THAAD anti-missile system shortly before her impeachment last year.

A THAAD unit previously stationed at Fort Bliss in Texas moved to South Korea with a full complement of six truck-mounted launchers, each with eight interceptor missiles, an AN/TPY-2 radar unit and associated command and communications facilities.

Poor communication

The THAAD unit in South Korea reached its initial operational capability in late April after the US brought in two launchers in early March. Four additional launchers have since arrived in South Korea to add to the system for full deployment.

The arrival of the four additional launchers became a top political issue in South Korea following revelations the defense ministry deliberately omitted the fact in a report to the office of new President Moon Jae-in.

That raised allegations of a cover-up, with Moon expressing frustration and ordering an investigation into how the omission happened. The probe determined that a senior defense ministry official ordered the deletion of the four launchers' arrival from the report.

Analysts here believe the problem may have been one of poor communication between the defense ministry and the new administration, compounded by a media backlash against the decisions of the previous government and vocal opposition from people living near the deployment site.

Read: China, Japan wary of each other over advanced missile radars

"I really think there has been an overreaction in the domestic media here," said Daniel Pinkston, a professor of international relations at the Seoul campus of Troy University.

"Moon has not had the luxury of a transition period into the presidency, he has a huge domestic agenda and there is only so much he can handle," Pinkston told DW.

"My impression of his predecessor is that Park delegated a lot of tasks to people that she trusted and the details of the THAAD deployment would have been left in the hands of the generals and retired generals in the ministry."

Pinkston speculates that "a big splash" was made to the media when the first two launcher units were deployed at the golf course, but that there was no attempt at subterfuge when the remaining four launchers were simply left in storage.

"There is a dispute over whether the military deliberately fudged the numbers, but I believe it was probably more a case of sloppiness because these officials had been given such freedom to operate under Park," he said. "And then it was seized upon by the media and the anti-THAAD factions and made out to be something sinister and secret."

'Blown out of proportion'

Stephen Nagy, a senior associate professor of international relations at Tokyo's International Christian University, agrees that the matter had been "blown out of proportion." He adds, however, that Moon may be able to make significant political capital out of delaying the THAAD deployment.

"Moon is trying to differentiate himself from his predecessor, to show that he is clean and that will help to build his political base," he said. "Slowing down the deployment will also allow South Korea and China to rebuild their relations and potentially give Beijing the opportunity to lift the punitive economic sanctions it has imposed since Seoul announced it would deploy THAAD.

"That will also play well to a large part of the domestic audience because they will be the ones who feel the positive economic benefits of renewed trade with China," he added.

But Moon may have a harder time with his US allies, with Senator Dick Durbin warning in late May that Washington might divert the money for THAAD to other areas that more directly ensure the security of the US if Seoul makes it difficult for the system to be deployed.  

"The US trusts the ROK official stance that the THAAD deployment was an Alliance decision and it will not be reversed. We will continue to work closely with the ROK Government throughout this process," Cmdr. Gary Ross, a Pentagon spokesman, told Yonhap News Agency.

"We have worked closely and have been fully transparent with the ROK government throughout this process. US Forces Korea confirmed in May 2017 that the Terminal High Altitude Area Defense (THAAD) system is operational and has the ability to intercept North Korean missiles and defend the Republic of Korea," he said.

Army Chief of Staff Gen. Mark Milley said the US will "work through the issue." 

"The THAAD is essential to protect US forces in Korea, but also South Korea as a whole and US forces in Korea are there in order to protect the entire country. So we'll work through that," Milley said.

And with a summit between Moon and US President Donald Trump coming up, Pinkston believes that the issue could be a sticking point.

"It could affect the alliance and, potentially, the issue could snowball very quickly if Trump takes offence to Moon's position," he said.