The Department of Transportation is working with Citi Bike's operator on a "holistic deal" to fix the snags that have kept the city's bicycle share system spinning its wheels a year after its debut.

DOT Commissioner Polly Trottenberg said Tuesday negotiations with Alta, the Portland, Oregon, bike share operator behind Citi Bike, continue in an effort to improve hardware maitenance, how bike docks are balanced and ensure that the company is well funded.

"They're making some progress," Trottenberg told reporters. "We're hopefully negotiating a larger package which will really address some of the operational issues ... and how we go forward with expansion."

NYC Bike Share and its parent Alta have been seeking millions of dollars from investors to expand. Despite the operational and software problems the bike share system has faced in the past year, Citi Bike has clocked more than 8.75 million trips and has more than 104,000 annual members. NYC Bike Share did not return a request for comment.

"We want to make sure that Alta is capitalized, that they have strong management, that they have a good staffing plan, again, to address things like the rebalancing of the bikes, the maintenance of the bikes, and to get their software problems fixed," Trottenberg said.

The DOT chief also denied a Wall Street Journal report that said the city told Alta that it owes $1 million to cover lost revenue from the parking spots docks occupy, saying that a "hard and fast number" doesn't exist. Trottenberg on May 15 told reporters that she was open to renegotiating the contract between the city and Alta on owed parking revenue and sharing profits.

"At the moment, we're not handing them a bill," Trottenberg said when asked about the WSJ report. "We're trying to sit down and work with them to come up with a system that's going to work moving forward."