WASHINGTON — President Barack Obama signed legislation Tuesday that affords greater protection to federal employees who expose fraud, waste and abuse in government operations.

Capping a 13-year effort by supporters of whistle-blower rights, the new law closes loopholes created by court rulings, which removed protections for federal whistle-blowers. One loophole specified that whistle-blowers were only protected when they were the first to report misconduct.

Obama also signed legislation that protects U.S. airlines from having to pay into a European Union program to cut down on pollutants. Earlier this month, the EU postponed its enforcement of the payment for non-EU airlines amid protests from numerous countries and threats of a possible trade war.

The whistle-blower law makes it easier to punish supervisors who try to retaliate against the government workers.

The federal official who investigates retaliation, Special Counsel Carolyn Lerner, said her office “stands ready to implement these important reforms, which will better ensure that no employee suffers retaliation for speaking out against government waste or misconduct.”

The new legislation, however, would go beyond restoring protections, to expand whistle-blower rights and clarify certain protections. For example, whistle-blowers could challenge the consequences of government policy decisions.

Specific protections would be given to certain employees, including government scientists who challenge censorship. Workers at the Transportation Security Administration, who provide airport security, would be covered under the law for the first time.

The law also would clarify that whistleblowers have the right to communicate with Congress.

To stop illegal retaliation, the law would make it easier to discipline those responsible, by modifying the burden of proof required when taking action against those trying to punish whistle-blowers. Also, the Office of Special Counsel, which was established to protect federal employees, would no longer be liable for attorney fees of government managers if the office does not prevail in a disciplinary action.

The new law would suspend the Federal Circuit Court of Appeals’ sole jurisdiction to review decisions in whistle-blower cases.

The law’s supporters said the court consistently narrowed protections and ruled for whistle-blowers only three times in 229 cases between October 1994 and May 2012. A review by all federal circuit courts was added as a two-year experiment.

Tom Devine, legal director of the Government Accountability Project, said, “This reform took 13 years to pass because it can make so much difference against fraud, waste and abuse. Government managers at all levels made pleas and repeatedly blocked the bill through procedural sabotage.”

Devine, whose organization represents whistle-blowers, said the bill sailed through Congress once some senators who previously worked in secret to block a vote dropped their opposition.

The new airlines law was a response to an EU program that places a cap on carbon dioxide emissions from industrial polluters. Early this year, the law was expanded to include all airlines flying into and out of Europe.

U.S. airlines complained that they would be charged even for the emissions discharged over the United States or the Atlantic on their way to European destinations. The U.S. industry says it would cost it some $3.1 billion between 2012 and 2020. Those payments were to start in April, but the EU postponed that earlier this month.

“Although European leaders have temporarily pulled back their tax proposal, the law signed by the president today will help ensure the EU scheme will not resurface next year like a phoenix rising from the ashes,” said Rep. John Mica of Florida, the Republican chairman of the House Transportation Committee,

The airlines emissions legislation requires the transportation secretary to prohibit U.S. airlines from paying into the EU emissions program if that prohibition is deemed in the public interest. It also urges the administration to engage in international talks to seek a global approach to aircraft emissions.

“The Obama administration should seek binding regulations and limits on such pollution when it meets with international partners to establish these rules at the International Civil Aviation Organization,” said Sarah Saylor of the environmental group Earthjustice.

Obama also signed legislation that permits construction of a natural gas pipeline within certain areas of the Gateway National Recreation Area in New York City.

He also signed into law legislation that sets a cost-of-living adjustment for veterans who receive disability compensation. The increase is estimated to amount to about 1.9 percent.