The cash-strapped MTA will run fewer buses on Brooklyn’s busiest route — but the ones it does send will be roomier, the agency announced Thursday.

The change to the B46 route — which is expected to add a few minutes to waits at all times except weekday mornings, but create more space for riders on the buses themselves — has been framed as a cost-cutting “service enhancement,” but critics say longer waits mean poorer service, full stop.

The MTA plans to shift the bustling route from 40-foot buses to less frequent 60-foot “articulated” buses, which carry 35 percent more passengers, in a move expected to save the authority $2.4 million.

“We are more nimble and responsive with the way we manage our bus operations and use new fleet technology, which results in better and cost-efficient service for our customers,” said MTA bus boss Craig Cipriano.

But while wait times on morning buses — which currently operate at 108 percent capacity — will hold steady, riders on the notoriously-overcrowded Utica Avenue line will see less frequent service at all other times.

Midday buses will shift from every six to every nine minutes, afternoon peak buses from three to five minutes, and evening buses from five to seven minutes.

During the afternoon rush, that will mean just 12 buses per hour as opposed to the current 20.

The changes earned jeers from transit advocates, who rallied Thursday morning against previously announced Brooklyn bus service reductions.

“Riders don’t want to wait longer for buses and trains. For our city to thrive, we need frequent, reliable transit service,” said Riders Alliance spokesman Danny Pearlstein.

City buses have been hemorrhaging riders for over a decade, thanks to blistering traffic congestion, infrequent service and outdated routes based on century-old streetcar lines.

To increase ridership, transit advocates and union leaders have called for shorter wait times and more dedicated bus lanes on the most congested routes.

But faced with massive future operating deficits, the MTA has done the opposite — making a series of minor bus cuts over the course of 2019, most recently to Brooklyn’s high-ridership B38, B54 and B15 lines. Agency officials have warned that more cuts may be on the way.

“Whenever you increase headways — that’s not a service enhancement. That’s a service cut,” said J.P. Patafio, who leads Transport Workers Union Local 100’s bus division. “This isn’t an enhancement. They’re pushing this into a death spiral. You’re killing the service.”

Experts say the benefits of longer B46 buses are ambiguous.

“Outside of the morning commute, it looks like the crowding isn’t going to get much better or worse, but waits will be a little longer,” said Ben Fried of the Manhattan-based TransitCenter think tank.

In addition to the changes on the B46, the MTA also announced small service additions on the S53, S93, Q55 and Q28 at a total cost of $300,000.

“It’s no secret that the MTA is in a dire financial situation, and we are required to balance our operating budget,” MTA rep Amanda Kwan said in a statement. “Today we announced that we’re increasing service on routes that benefit tens of thousands of riders in Queens, Brooklyn and Staten Island, while saving money. Who wouldn’t be in favor of that?”