Lewis told the BBC that he was "shocked" at the volume of material on the computer and that he had "no doubt whatsoever" that the images had been accessed by Green.
This latest revelation will heap further embarrassment on Green and May, whose government is already facing attacks on multiple fronts.
Green is already the subject of a government investigation after he was accused by journalist Kate Maltby of making unwanted advances toward her during a meeting in 2015. Green has described those allegations as "completely untrue" and "deeply hurtful."
The latest revelations follow a story in story in the Sunday Times last month alleged that "extreme" pornographic material had been found on Green's computer.
Green denied the stroy when it was published, saying it was "completely untrue and comes from a tainted and untrustworthy source."
Lewis says was surprised at Green's denial, and had come forward in support of the Sunday Times source, another senior retired police officer. Lewis said he carried out the raid at Green's office and examined the computer himself.
He said that Green's denial of the original allegations was "quite amazing" and said he felt compelled to speak out.
"The computer was in Mr Green's office, on his desk, logged in, his account, his name," said Lewis told the BBC.
"In between browsing pornography, he was sending emails from his account, his personal account, reading documents ... it was ridiculous to suggest anybody else could have done it."
Lewis added that none of the images found were "extreme" but that analysis of the computer suggested that they had been viewed "extensively" over a three-month period, sometimes for hours at a time.
A spokesman for Green, who holds the title of First Secretary of State, said he would not comment on the latest claims. "It would be inappropriate for Mr Green to comment on these allegations while the Cabinet Office investigation is ongoing; however, from the outset he has been very clear that he never watched or downloaded pornography on the computers seized from his office.
"He maintains his innocence of these charges and awaits the outcome of the investigation."
Another Conservative MP, Andrew Mitchell, questioned why Lewis had come forward. "I think it is highly questionable whether a retired police officer should misuse this sort of material in this way and I think the police need to explain why there was any record kept of entirely legal activity," he told the BBC.
In his BBC interview, Lewis rejected suggestions that Green's computer might have been hacked, saying: "It would be a very bizarre situation for somebody to hack a parliamentary computer to place pornography."
"The shocking thing, as I was viewing, I noticed a lot of pornography -- thumbnails -- which indicated web browsing. "There were a lot of them. I was surprised to see that on a parliamentary computer. I had to take a step back, because I wasn't expecting that. When you ask me a number, I couldn't tell you. There were thousands."
Lewis also rejected claims somebody else could have been viewing the material on Green's computer, saying: "It was so extensive, whoever had done it would have to have pushed Mr Green to one side to say 'Get out, I'm using your computer'."
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