The club announced it is ending its seven-year agreement with the Penny Street firm after making a deal with Dutch-company Heineken to supply Ewood Park’s bars.
Blackburn MP Jack Straw branded the decision as ‘ridiculous’ and ‘short-sighted’.
And community leaders said the club and its owners, Indian chicken giants Venky’s, should be supporting a local firm, especially in the current economic climate.
The new deal, which Rovers said would improve the matchday experience for supporters, will run until 2017.
The agreement sees Foster’s continue as the main lager on offer in the stands, which will now be supplied by producer Heineken after previously being bought in by Thwaites.
John Smith’s Extra Smooth will be the bitter option available.
Cask ales, such as Deuchar’s IPA and Theakston Lightfoot, will be available in the Blues Bar.
MP Jack Straw condemned the decision as a ‘mistake in judgment’. He said the club should be supporting local businesses and jobs.
He said: “It is another mistake by a management team that is completely out of touch.
“They really do seem to have the opposite of the Midas Touch.
“Thwaites’ beer is infinitely better than that provided by Heineken.
“It is a ridiculous, silly and short-sighted decision.”
Blackburn with Darwen Council leader Coun Kate Hollern said the club should not be taking business out of the town.
She said: “Rovers should be supporting a Blackburn company.
“At the moment, where possible, we want local people to benefit from local decisions.
“But this just makes you wonder whether Venky’s have any interest in the community in Blackburn.”
Rovers fan Rick Boardman, of Darwen, said he understood the move from a business perspective.
He said: “I guess they have gone with the cheaper deal, but it is sad a local company loses out.
“Thwaites is one of the biggest and most historic firms in town so for it not to be involved with Rovers is a shame.
“I think a lot of people wouldn’t mind paying that little bit more if it meant supporting a local business.”
Phil Thompson, of Blackburn Rovers Football Club Action Group, said: “I don’t understand why it has been done.
“You would hope more support would be shown for a local company and that local suppliers would be the priority in this situation, especially in the current economic climate.
“It is disappointing.”
A spokesman for Thwaites said: “Thwaites has commercial pouring rights deals with a number of football clubs in the North West.
“We submitted a deal to Blackburn Rovers and on this occasion they have decided to go with a different supplier.”
Rovers head of commercial and marketing Greg Coar said Blackburn Rovers thanked Thwaites for an ‘excellent and supportive relationship’ over the past seven years.
He said: “Our aim is always to improve the fans’ enjoyment of coming to Ewood.
“The choice, quality, speed of service and price of the beer on offer is often an important part of that.
“We believe the choice of brands that Heineken offers, plus the investment in updating the dispensing of their products, will ensure the concourses, executive lounges and Blues Bar continue to provide a fantastic service for our guests and supporters.”
Heineken UK spokesman David Jones said: “Heineken is delighted to become the exclusive supplier of cider and beer at Ewood Park.
“The new partnership will give Rovers fans and visitors to the stadium the opportunity to enjoy a range of our market-leading draught and packaged brands in concourse bars and executive lounges throughout the ground.
“The agreement strengthens the association we curently enjoy with football through Heineken’s sponsorship of the UEFA Champions’ League and a number of commercial partnerships with leading Championship and Premier League clubs in England and Wales.”
Thwaites will continues as the official beer supplier for Burnley FC.