The Blues boss admitted his team is running on empty after eight games in 26 days with a squad of only 13 fit senior outfield players for most it.
And the toil of that has eventually caught up with them at a time when the Fratton faithful were hoping for a rousing end to the season.
Realistically, Pompey needed to beat Wycombe to maintain a serious interest in the race for the play-offs.
A draw against Ipswich and a midweek defeat at Plymouth had severely dented those hopes over the past seven days – meaning anything less than a win against Gareth Ainsworth’s wily Wycombe would be a telling blow.
But that’s exactly what Pompey served up as they failed to test visiting keeper David Stockdale to warrant a victory.
Indeed, it was the visitors who showed more attacking purpose as they recorded 15 shots and four on target to the home side’s six and one total.
Cowley attempted to freshen his team up by making four changes to the side that lost at Home Park.
That included recalls for Marcus Harness and Tyler Walker in attack.
Yet Pompey’s lack of spark in that area let them down they as the game ended goalless.
And Cowley was quick to point out why.
Speaking to Radio Solent at the final whistle, he said: ‘We’re disappointed today.
‘I thought we were flat. I didn’t think we played with the energy and intensity that we wanted to.
‘As a consequence, we didn’t have with the purpose to our play.
‘We know Wycombe are a powerful team, a team that has just come down from the Championship.
‘They recruited in the Championship, so they’ve got a lot of good players with athleticism and power and a real directness.
‘You have to earn the right against them, and then you have to be courageous enough to take the ball, and I don’t think we did that.
‘As a consequence I don’t think we got into enough areas and when we did we lacked that creative spark.’
With Pompey now heading into a two-and-a-half week break due to games against Bolton and Rotherham needing to be rearranged, Cowley added: ‘Defensively it was a pretty good display, but offensively – in a game that we really wanted to win, we looked tired, we looked tired!
‘It’s not for me to be too critical because we’ve been going Saturday, Tuesday, Saturday, Tuesday, Saturday with 13 senior fit players.
‘We thought we could freshen it up at the top end and it was certainly nice to have Marcus Harness and Michael Jacobs back available.
‘I certainly felt we were able to change the game from the bench today which maybe we haven’t been able to do in recent weeks, but we didn’t do enough.’