The hacking occurred in March and the perpetrators appeared to be targeting the files of people who had applied for top-security clearances, the Times said, quoting senior US officials.
The report came as US Secretary of State John Kerry was in Beijing for two days of high-level talks on thorny issues including hacking.
In the new case, the intruders accessed some of the databases of computers at the Office of Personnel Management before authorities caught wind of their presence and blocked them, the newspaper said.
The paper quoted one senior US official as saying the attack was traced to China although it was not clear if the hackers belonged to the government.
Hackers try to breach US government computers nearly every day but rarely succeed. The Office of Personnel Management case stands out because that time they did get in, the Times said.