The breach is said to have taken place in mid-February and occurred at the Division of Structural Biology, known as Strubi, which has been carrying out research into the virus.
Strubi is distinct from the Jenner Institute, which develops the Oxford vaccine in partnership with AstraZeneca.
The university confirmed there had been a hack and said it was investigating.
“We have identified and contained the problem and are now investigating further,” an Oxford spokesman said.
“There has been no impact on any clinical research, as this is not conducted in the affected area.”
Oxford was working with the National Cyber Security Centre (NCSC) on the incident, the spokesman added, but did not name the facility affected.
The Telegraph quoted security sources as saying it was unclear who was behind the attack and that they could not rule out a hostile foreign state.
NCSC, the cyber security arm of spy agency GCHQ, did not immediately respond to a request for comment.
Digital espionage targeting health bodies, vaccine scientists and drugmakers has surged during the pandemic as hacking groups scramble to secure the latest information on the outbreak.
In December, US drugmaker Pfizer and its German partner BioNTech disclosed that documents related to development of their Covid vaccine had been “unlawfully accessed” in a cyberattack on Europe’s medicines regulator.