The public agency building the Transbay Transit Center says it will keep pumping groundwater from beneath the construction site well into 2017, despite claims the process is contributing to the sinking of the Millennium Tower next door.

The Transbay Joint Powers Authority said the dewatering, which is performed to maintain a dry work site, would continue for the foreseeable future at the $4.5 billion transit center.

“At some point prior to completion of the transit center in late 2017, construction will have progressed to the point that the weight of the transit center is sufficient to counterbalance the upward water pressure, and dewatering can cease,” the authority said in a statement.

The statement comes after executives with Millennium Partners, which built the 419-unit luxury condominium tower at First and Mission streets, accused the authority of “a pattern of reckless behavior” that has caused the 58-story building to sink 16 inches and tilt 2 inches to the northwest at its base.

In particular, they said the water table under the high-rise has dropped at least 20 feet since construction started on the transit center in 2012. The dewatering caused the compression and weakening of the soil under the tower’s foundation, Millennium contends. The tower, at 301 Mission St., opened in 2009.

The joint powers authority blames the Millennium Tower’s settling on the developer’s decision to drive “friction piles” 66 feet to 91 feet long rather than the 200-foot piles needed to go into bedrock. It said the sinking issues at the Millennium Tower were apparent before construction started on the transit center.

“There is no evidence to support Millennium Partners’ claim that the TJPA’s dewatering is the cause of the excessive vertical settlement and tilting of the Millennium Tower,” the authority stated.

On Wednesday, Millennium attorney Peter Meier demanded the joint powers authority “cease and desist from further dewatering and any construction activity that is adversely affecting” the tower. Millennium said that it would seek a judicial intervention to stop the removal of water from the job site if an agreement isn’t worked out with the agency.

Millennium also accused the authority of misleading the public about when its construction crews started dewatering the property. While the authority said dewatering didn’t start until 2013, Millennium said city building permits and photographs show it started in 2011.

Meier accused the authority of “misleading” the public on the timing of the dewatering activities “in an effor to avoid responsibility for the resulting subsidence of 301 Mission.”

“TJPA knows the significance of the timing for when it started dewatering near 301 Mission St. because ... it caused a precipitous drop in the water table under 301 Mission that continued at least through 2015,” Meier said.

The agency argued that the dewatering has had limited impact on its next-door neighbor because the transit center is separated from adjoining properties by a shoring wall that extends into clay 90 feet below the surface.

“The TJPA’s wall and the layer of old bay clay significantly limit the impact of the TJPA’s dewatering on adjoining properties,” the agency asserts.

The Transbay Transit Center is scheduled to open next year as a replacement for the old Transbay Terminal. It will be a hub for numerous bus services and could one day house a California high-speed rail station and a downtown extension of Caltrain.

J.K. Dineen is a San Francisco Chronicle staff writer. Email: jdineen@sfchronicle.com Twitter: @sfjkdineen