The National Intelligence Service (NIS) said Suh Cheon-Ho, one of its three vice-chiefs, stepped down to take responsibility for the involvement of his staff in the scandal.
The agency has been 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 North Korea in 2004.
State prosecutors launched a probe in February when China confirmed that the documents were not authentic, and NIS chief Nam Jae-Joon has come under pressure from politicians and human rights activists to step down.
The two-month investigation uncovered no evidence that top NIS officials had been involved, it said.
Charges have however been brought against two NIS agents, including Lee In-Cheol who served as a South Korean consul in China's northeastern city of Shenyang.
A third NIS official was indicted two weeks ago.
Suh, in charge of intelligence-gathering and investigating North Korean spies, issued a public apology for the "disgraceful" scandal.
"I submitted my resignation to assume all responsibility," he said in a statement released by the NIS.
She called for a thorough investigation last month after an NIS informant linked to the forgeries tried to commit suicide. He survived and was arrested by prosecutors.
With local elections due in early June, the case has been a politically sensitive one for Park, who appointed Nam a year ago.
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.
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