SEOUL (AFP) - South Korea's intelligence chief vowed a "bone-crushing" overhaul of his embattled agency as he apologised on Tuesday for a scandal that saw senior agents charged with fabricating evidence in an espionage case.

"I feel deeply pained for letting this happen ... and feel tremendous responsibility," Nam Jae Joon told reporters in a rare press appearance.

His apology came a day after the agency's deputy chief stepped down.

The National Intelligence Service (NIS) was accused of forging documents - including Chinese border control records - to build a false spying case against a former Seoul city official who had escaped to South Korea from the North in 2004.

State prosecutors launched a probe in February when China confirmed that the documents were not authentic, and Nam came under intense pressure from politicians and rights activists to step down.

But Seoul prosecutors on the case concluded on Monday that they did not believe the forgery was part of a larger operation orchestrated by the NIS leadership.

So far charges of fabricating evidence have been brought against three NIS agents.

Another agent attempted suicide last month during the prosecutors' probe and he will be charged when released from hospital, prosecutors said Monday.

Nam vowed to overhaul the agency's investigative methods in line with "changing times" and to win back public trust.

"We will take this opportunity to re-evaluate our investigative methods, root out wrong customs and conduct a bone-crushing overhaul of our system, so that things like this will never happen again," he said.

But he also warned of the dangers of undermining the NIS at a time of heightened military tensions with North Korea.

Since February, the North has test-fired dozens of short-range missiles and two mid-range missiles, and also threatened to conduct another nuclear test.

"I feel tremendous grief that the NIS - the bulwark of our national security - is being shaken like this in such a grave time," Nam said, pleading for public support.

The spy agency - which has changed titles over the years - had a particularly notorious reputation in the decades of authoritarian rule before South Korea embraced democracy in the 1980s.

The modern-day NIS has also been tainted by a series of scandals, most recently the admission by some agents that they meddled in the 2012 presidential election.

Nam's predecessor as NIS chief, Won Sei Hoon, was convicted last month of taking bribes and jailed for two years.