The Pakistani team went through "an extraordinary schedule of 16 one-day matches in a row with no domestic four-day cricket for the players and that didn't help", said Woolmer, whose first Test as coach has been disappointing.
He however insisted he was not trying to put up an excuse for the lacklustre performance by the home team in the Test.
"We have had enough bad sessions to be on the wrong side of this game. Our batting was disappointing in the first innings, to say the least, and Jayasuriya played magnificently (even though) we bowled well in the morning," Woolmer said on Saturday.
Pakistan closed the fourth day of the first Test on a precarious 114-4, chasing a world record equalling 418 to win after Sri Lanka mustered 438 runs in their second innings spiced with a masterly 253 by Sanath Jayasuriya.
The home team faces a daunting task of either scoring 304 runs on Sunday to win or play out 83 overs to draw the Test.
"It's going to be tough work to save the game but we will have a go."
The 56-year-old Woolmer, who played 19 Tests for England before coaching South Africa between 1994-99, took charge in June this year after Pakistan great Javed Miandad's was replaced following home defeats against arch rivals India in April.
"The fact (is) that this is the first Test since April this year, so we have to get around that and do better than that in future," said the coach.
"I would like to see more Tests in the general programme, surely there should be three or four Tests and then five one-day internationals so that players can alternate in a better way."
Pakistan failed to seize the initiative after bowling Sri Lanka out for 243 in the first innings as they managed just 264 in reply which proved short. "We should have got more runs in the first outing and we all accept that. As a team we had a long discussion after the day's play and we will try to put it right," said Woolmer, under whom Pakistan have won 11 of the 16 one-day games.
Woolmer said he would like to see more first class matches to assess whether his players' inability to spend a long time at the crease in Tests was an endemic problem in the national cricket structure.