In various ethics agreements and financial disclosures she has filed since last 2016, Ms. Chao had said that stock options awarded during the nearly two years she served on the board at Vulcan would be paid out in cash — ending her financial ties to the company. Instead, those options were paid out last year in stock, which Ms. Chao held onto until this month, meaning she continued to have a stake in the industry.

The Transportation Department placed blame for the controversy on an unnamed accountant to Ms. Chao, who apparently told agency officials that she would receive cash instead of stock.

But in her own letter sent this week to the Office of Government Ethics, Judith S. Kaleta, the deputy general counsel at the Transportation Department and the agency’s top designated ethics official, said that the stock holding did not present a conflict. “Secretary Chao has not participated personally and substantially in any particular matter that has a direct and predictable effect” on Vulcan, which would be necessary if she had a certifiable conflict of interest, the letter said.

Ethics lawyers have said the holdings appeared to be a conflict of interest because even if Ms. Chao was not involved in contracting decisions that directly affected Vulcan, she helps set transportation policy. Given the critical role the Transportation Department plays in funding highway construction projects nationwide, that can have a major effect on the company’s bottom line, they said.

In recent weeks, Ms. Chao has been the focus of a series of news articles scrutinizing her actions since she took over the department, including a report in The New York Times about her interactions with her family, which owns a shipping company that does extensive business in China. A separate article in Politico examined the role one of Ms. Chao’s aides has played in helping coordinate federal highway grants to Kentucky, which her husband, Senator Mitch McConnell, a Republican and the majority leader, represents.