The Fratton Park legend is of the opinion the head coach remains hamstrung by an inability to move on certain high-earning players during the summer transfer window.
And that forced the former Lincoln manager to make sacrifices in the quality he eventually brought in during his Pompey overhaul.
Whittingham made the point after watching Saturday’s 4-1 humbling at Rotherham as a pundit for BBC Solent.
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The visitors crumbled in the second half to record their fifth League One defeat of the season – leaving Cowley’s men 12th in the table and four points off the play-off places, with Paul Cook’s Ipswich up next on Tuesday night.
Seven of the starting XI were players he recruited during the summer – while two more emerged from the bench as Pompey chased the game in the latter stages.
Yet Whittingham believes Cowley most likely had to compromise with the calibre of player he brought in in the summer.
And that’s because he was unable to shift high-earning contracted players that he didn’t fancy rather than not enough money coming his way from the owners.
Although, he did add that Cowley should share some of the responsibility, while players he showed faith in also need to step up.
Speaking from the New York Stadium, Whittigham said: ‘I do think they obviously want(ed) to get rid of some the big-hitters and free up some money that they have to generate themselves, but they weren’t able to do it and then they weren't given extra money.
‘Can you blame the Eisners for not putting in any more money in? I don’t think so at the moment.
‘We would all like them to spend more money but I don’t think we can actually say they haven’t put enough money in.
‘It’s a reasonable budget from what I’m made aware of and the Cowleys have just got to suffer the fact that players they don’t want have got long contracts.
‘As a result they haven’t been able to make the signings they wanted in crucial positions and have had to go for others.
‘Ultimately, the manager takes the responsibility, he signed the players that he’s brought in.
‘But the players have got to take the responsibility on the pitch.
‘At this moment in time these players, as a group, aren’t tough enough to beat.’
Cowley brought in 14 players during the summer, while he also added Jay Mingi to his ranks following the closure of the transfer window.
Chief executive Andy Cullen revealed last month that Michael Eisner made more money available to the head coach after the contracted players who remained following his close-season overhaul took up two thirds of the money originally made available.