Pietersen was axed from the squad with England director of cricket Andrew Strauss citing a “massive trust issue”, following their 0-5 Ashes series loss to Australia.
Now, Cook, who quit the captaincy on Monday, put the blame on the England Cricket Board (ECB) saying that the whole issue was not properly handled.
“I do wish it had been done differently. I felt it wasn’t handled particularly well by the ECB. I know I was the lightning rod for it, every person thought it was my decision. I felt I bore the brunt of that, unfairly in my opinion,” Cook was quoted as saying by dailymail.co.uk on Tuesday.
“I felt a little bit let down by the ECB in that one period, where they kind of let me out to dry a little bit. But that’s all gone now,” he added.
“I think we all have regrets over the way it was handled, but when Andrew Strauss came on board and made the final decision (Pietersen) wasn’t coming back, it made it a little easier.”
Commenting on the decision to quit as the Test captain after being in the role for more than four years, he said: “It was a tough decision but in one sense easier than I expected. The hard bit was giving it away and telling myself it was time to go, because it is such a brilliant job, but it was easy because I felt I was done.
“I’d been to the well a couple of times as England captain and I couldn’t go again. I’ve looked back a bit over the last couple of weeks knowing this was the end and I’m quite proud of what I’ve achieved,” he added.
In December, England lost to India 0-4 away.