"The majority of the people were killed and injured in crossfire and when people were trying to come into the army-controlled area. But we were ordered to exaggerate the figures," Dr V Shanmugarajah said.
The doctors said that fewer than 1,000 civilians were killed between late January and May 18, when the military declared victory in the more than two-decade-long civil war.
"Totally there were around 350 to 400 people killed from April 15 to May 15," Thurairajah Varatharaja, another doctor, said. He said another 300 to 350 civilians were killed and up to 650 were injured from late January to April 15.
Sam Zarifi, the Asia-Pacific director for Amnesty International, questioned whether the doctors' latest statement could be relied upon after weeks in custody.
"Given the track record of the Sri Lankan government, there are very significant grounds to question whether these statements were voluntary, and they raise serious concerns whether the doctors were subjected to ill-treatment during weeks of detention," he said.
"From the time the doctors were detained, the fear was that they would be used exactly this way."
The five men denied they were under pressure from the military to change their stories, but their new accounts differ dramatically from those of aid organisations and other international bodies.
"The information that the doctors have given in the press conference actually contradicts other credible sources such as the ICRC [International Committee of the Red Cross]," Miriam Young, director of the US counsel on Sri Lanka, an advocacy group which focuses on human rights, said.
"They now say the hospital was never shelled, when ICRC staff were in fact at the hospital at the time and can testify to that," she told Al Jazeera from Washington.
The United Nations estimates that about 7,000 civilians died in the fighting in the north of the Indian Ocean island between January and May.
When asked about the doctors' comments, Gordon Weiss, a UN spokesman, said: "We stand by our statements."
The Sri Lankan military has repeatedly denied all allegations that it was responsible for the deaths of civilians.
It was impossible to get a clear picture of events in the area as the military pressed forward against the separatists as journalists and aid organisations were barred from entering.