Rail officials have issued the contract to build the Honolulu transit project’s first three stations to Hawaiian Dredging Construction Co., more than three months after the firm submitted the lowest bid for that work.

The holdup in awarding Hawaiian Dredging’s $78.9 million contract to build three Waipahu-area stations will likely push the opening of the rail system’s first 10 miles, to Aloha Stadium, from June 2018 to sometime in September of that year, according to Honolulu Authority for Rapid Transportation Executive Director Dan Grabauskas.

The delay occurred after the second-lowest bidder, Nan Inc., unsuccessfully challenged Hawaiian Dredging’s low bid, arguing that Hawaiian Dredging’s estimated costs for compensation in the event of a delay were “unreasonable, unrealistic and false.”

Nan had submitted an $85.1 million bid to build the West Loch, Waipahu Transit and Leeward Community College stations. When HART rejected its challenge, Nan appealed to the state Department of Commerce and Consumer Affairs. However, the consumer affairs agency sided with HART last month.

The three stations had been part of a larger, nine-station group that went out to bid for construction last year. When those bids came in at least 60 percent over what HART had budgeted, the rail agency canceled them. HART then divided the stations into smaller groups, hoping the move would yield at least some cost savings.

For the original nine-station construction package, Nan had submitted the lowest bid to build — at $294.5 million. The firm initially protested HART’s move to cancel those bids but later dropped the protest.

Bids to build the rail’s next three stations, at East Kapolei, the University of Hawaii-West Oahu and Hoopili, will be opened Tuesday.