Pietersen also heaped additional pressure on out-of-form skipper Cook, claiming his lack of runs was playing on his mind and making him appear a "rabbit in the headlights".
"England were in winning positions in both matches but blew it, and I believe that is a symptom of the senior players being very unsettled," Pietersen, controversially dumped from the team in the wake of the Ashes debacle, wrote in his column in the Telegraph.
"They are not turning up for the captain or coach. (Stuart) Broad and (James) Anderson looked jaded at Headingley," added the South Africa-born batsman of the performance of England's fast bowling duet in the second test loss in Leeds.
"Why? Why was Jimmy so emotional? We have lost a lot of matches in the past but he has never shown such emotion.
"It says to me there is an underlying current of unhappiness. The Australia tour was hard. We were beaten up due to a lot of reasons I cannot go into right now, and some of the senior players are still suffering, with the result that they are struggling to offer leadership in the dressing room."
Pietersen said "fear of failure" appeared to be influencing England and Cook's tactics on field, as shown by the team's late declaration in the first test draw in Lord's and the choice to bowl first at Headingley after winning the toss.
"You can only kid the public for so long," he said.
"If you tell them this is a brave new dawn, that the team will play an aggressive brand of cricket and try to be positive, but then play the same old negative stuff, the supporters will soon turn away from the team in droves."
Opening batsman Cook had been a "brilliant" player for England, but had few people in the dressing room to turn to help pull the team out of its funk, Pietersen added.
"I saw in Cook at Headingley the same look (former captain) Andrew Strauss had when he played his last test at Lord's," he said.
"He was a rabbit in the headlights. It was a shame to see Cooky looking that way."
The 34-year-old's dissection comes a day after former Australia spinner Shane Warne, a vocal critic of Cook's captaincy and a former team mate of Pietersen at Hampshire, urged the 29-year-old to either step down or take a break from the game in the same newspaper.
Cook has shown himself vulnerable to the criticism, saying he felt it was personal and that "something needs to be done" about it.
Pietersen reserved some praise for England's promising young brigade, with Gary Ballance, Sam Robson, Joe Root and Moeen Ali all scoring centuries in the series.
"A winning dressing room is a happy dressing room," he said.
"If they are given the opportunity the young players will learn to win and the corner will be turned."
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