The state commerce agency Tuesday threw out one of the two protests to the city’s billion-dollar rail car contract award. 

Bombardier Transportation filed an appeal with the state Department of Commerce and Consumer Affairs, after its protest to the contract was denied by the city last month. 

The Canada-based company’s argument centered on language in the proposal regarding limited liability. In its best and final offer, the company offered to change the language to have a cap on potential liability. As a result, the company’s bid was considered disqualified. 

Bombardier has argued that city officials never informed the company of the potential deficiency. But on Tuesday, senior hearings officer David Karlen said the company should have filed protests during the bidding process to protest the language. 

"(The city) did in essence say they’re not going to accept any changes," Karlen said. "We have a bidder saying, ‘I’m excluding these liabilities that everyone else is facing.’"

Karlen said that is why the city received higher offers from the other two companies, winning bidder Ansaldo Honolulu with a $1.4 billion contract, and the other losing bidder, Sumitomo Corp. of America, with a $1.45 billion contract. 

"The other offers are based on a much larger assumption of liability," Karlen said. 

Bombardier Transportation Vice President Andy Robbins said through a spokesman that the company will wait for Karlen’s written decision before determining what to do next. 

The company still has 10 days to file an appeal with Circuit Court. 

Today Sumitomo Corp. of America will have its day during an administrative hearing at the state Commerce and Consumer Affairs Department. 

Sumitomo executives have argued that their company scored higher on most aspects of the project other than price, and that they boast an overall lower operation and maintenance cost structure, even though their bid is more expensive than Ansaldo’s over the life of the contract.