WASHINGTON – The nation’s passport headaches may be easing a bit, but now comes the bill: almost $1 billion.

New travel rules that swamped passport offices and frustrated U.S. travelers this summer will cost the government an estimated $944 million over three years, according to federal paperwork filed Wednesday.

That amount is more than three times the State Department’s estimate for the first three years.

To raise the extra dollars, the department wants to keep a larger share of what U.S. citizens pay to get a passport – $20 of the nearly $100 fee for first-time applicants instead of $6.

Kurtis Cooper, a State Department spokesman, said the new proposal will not increase the cost of passports to the public.

The department initially figured it would cost $289 million between budget years 2006 and 2008 to handle the boost in demand for passports created by post-9/11 security measures passed by Congress and implemented by the Homeland Security Department.

Now, the passport rules are expected to cost $944 million in budget years 2008 to 2010.

The new cost estimate stunned members of Congress.

“Incompetence and poor planning have not only inflicted high costs and personal angst on consumers, but are now likely to cost the State Department itself an astounding amount,” said Sen. Charles Schumer, D-N.Y. “Let us hope Homeland Security and the State Department can improve their coordination and avoid egregious mistakes.”

This year’s surge in passport applications stems from new rules that went into effect in January requiring U.S. travelers to carry passports when flying to Canada, Mexico and the Caribbean. A similar requirement is to go into effect for all land and sea crossings next year.

Those rules caused a stampede that caught government officials flat-footed, as the State Department couldn’t handle the workload and the Homeland Security Department refused to budge on the security rules. During the worst of the delays in late spring and early summer, some applicants who would normally expect to wait six weeks for a passport found they had still not received them after 12 weeks or more.

Last month, the State Department said the processing time was down to about 10 weeks.

The problem was so bad that it spilled over into Congress. Many lawmakers reported their offices were deluged with hundreds of pleas from constituents desperate for last-minute intervention before their travel plans were ruined.

As a result, DHS eventually eased or delayed its requirements, and the State Department was forced to take drastic and expensive measures to trim the backlog, hiring hundreds of additional personnel and paying some employees to return to the U.S. from overseas to handle the paperwork.

Last year, the agency processed 12.1 million passports. This year, officials expect to process about 18 million.

When challenged by Congress, State Department officials said they were surprised so many Americans complied with the new law.