Saints director of rugby Jim Mallinder confirmed the news following his side's 25-23 defeat at London Irish.
England international Brookes, 25, had surgery on Thursday after suffering an injury against Racing 92 in the European Champions Cup.
"It's a big blow for us as he's been playing well all season and will be out for quite a while," Mallinder said.
Brookes, capped 15 times by his country, joins fellow prop Alex Corbisiero on Northampton's injury list.
Hooker Dylan Hartley did return for Saints at the Madejski Stadium on Boxing Day, lasting 60 minutes in his first appearance since 7 November having recovered from concussion.

Former multi-millionaire pig farmer Robert Pickton was convicted in 2007 of murdering six women. Charges relating to 20 other deaths were suspended.
Another inmate helped him smuggle the book out of prison, CTV reported.
The publisher requested its removal from retailer Amazon and apologised to victims' families, reports said.
Officials in British Columbia had earlier vowed to prevent Pickton, who says he is innocent, from profiting from sales of the memoir, entitled Pickton: In His Own Words.
"It is not right that a person who caused so much harm and hurt so many people could profit from his behaviour," said the province's Minister for Public Safety, Mike Morris, in a statement.
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British Columbian officials also asked Amazon to stop selling the memoir, which was published by Colorado-based Outskirts Press, a firm that specialises in helping authors self-publish books.
Amazon users had also called for it to be removed and gave it the lowest possible rating. The company has not yet commented on the book's appearance on its site.
Canadian Public Safety Minister Ralph Goodale said an investigation had been launched into how Pickton's manuscript was smuggled out of the maximum security Kent Institution prison where he is being held.
But CTV reported that Pickton bypassed checks on his own correspondence by passing the book to a fellow inmate, who sent it to a friend.
In the book, the serial killer said he was innocent and was framed for the killings by Canadian police, the Vancouver Sun reported.
Ernie Crey, whose sister Dawn's DNA was among that of 33 women found at Pickton's Port Coquitlam pig farm, said he was "deeply troubled" by the book.
Lori Shenher, who helped bring Pickton to justice and wrote her own book on the case, wrote that she hoped people would ignore it "in the interest of common decency".
Pickton was sentenced to life in prison with no chance of parole for 25 years after initially being charged with the murders of 26 women from a total of 69 who had gone missing.
He killed the women at his farm and fed some of their remains to his pigs.
During the trial, prosecutors claimed Pickton had confessed to 49 killings to an undercover police officer posing as a cellmate.
Northampton prop Kieran Brookes is set for an extended spell on the sidelines after having an operation on his knee.
[NEXT_CONCEPT]
A memoir apparently written by a Canadian serial killer has been withdrawn within hours of appearing for sale online.