On Tuesday, Chao cast the move as one of fairness, saying New York and New Jersey "need to step up and bear their fair share."
But Democrats and some Republicans say Trump's real motivation is to knock Schumer, who — among other battles with the president — is opposing Trump's long-sought wall along the U.S.-Mexico border. Like Gateway, the border wall is a contentious issue in ongoing talks on a $1.3 trillion catchall spending bill on which Schumer is a key negotiator.
Trump, whose home is in Manhattan, appeared to support Gateway at a friendly White House meeting last fall attended by New York Gov. Andrew Cuomo, Schumer and others.
"In the meeting he was good," Schumer said.
"The president made a commitment on Gateway. This isn't some New York project. This is the entire country and it would be really disastrous not to go ahead with it — especially if it's based on some vendetta against Chuck Schumer," said Rep. Peter King, R-N.Y.
The House has approved $900 million for the project, which is also a top priority of House Appropriations Committee Chairman Rodney Frelinghuysen, R-N.J. Schumer is also playing a strong hand in talks on the measure, but Trump's signature is required to enact it. The measure is slated for a vote later in the month.
The existing tunnel was damaged during Superstorm Sandy in 2012 and is nearing the end of its useful life. The Obama administration supported the project and the Trump team acknowledges that it is much needed.
"They are two of the richest states in the country. If they absorb all these funds there will be no other funds for the rest of the country," Chao said.
The New York and New Jersey delegations say the states are willing to put up half of the project's cost.
"Here are the facts: New York and New Jersey have agreed — because I helped get them to do it — to put up 50 percent of the funding for the project," Schumer said. "So the states have really stepped up to the plate. It's the feds who haven't."
Chao, however, says there's no documentation for such a deal. Her agency says the states have discussed ways to use other federal funding to cover the project's cost.
Sen. Susan Collins, R-Maine, chair of a key Senate panel with responsibility to fund transportation projects, says she supports putting enough money into the budget to pay for Gateway but not explicitly "earmark" the money. So-called earmarks have been banned, though Frelinghuysen found a way to do so without explicitly running afoul of the rules.
"Our approach is to avoid earmarks but fully fund accounts now that we have some additional funding and then the competitive process will go forward," Collins said.