The official price tag for La Guardia Airport’s overhaul has risen to $5.3 billion—more than $1 billion higher than previous estimates—as officials grapple with how to pay for major transit projects in the region.

The new tally accounts for increased cost estimates related to a looming project to replace La Guardia’s Terminal B and redevelopment work that stretches back more than a decade. A capital-spending plan from 2014 pegged the cost of the airport renovation at $3.6 billion, and more recent projections hovered around $4 billion.

The revised figure, which was released late Friday, comes amid growing tension inside the Port Authority of New York and New Jersey, the airport’s operator, as officials consider replacing its aging Midtown Manhattan bus terminal and digging two new Hudson River rail tunnels.

Transforming the airport, which has often been ridiculed by officials because of its dilapidated state, has become a priority for New York Gov. Andrew Cuomo, a Democrat, who controls the bistate agency along with New Jersey Gov. Chris Christie, a Republican.

But the arithmetic behind the evolving estimates for La Guardia’s overhaul has become a source of friction inside the Port Authority, with some officials growing frustrated as they seek clarity on the project’s costs, people familiar with the matter said.