Counterterrorism officials in the U.S. and the Middle East, who in recent years have shut down several Islamic charities accused of financing terrorist organizations, now are pursuing what they describe as a second constellation of such groups.

Key figures who avoided the initial legal dragnet in 2001 and 2002 have continued to raise funds that help Islamic militants in the Palestinian territories, Iraq and other conflict areas, counterterrorism officials in Washington and the Middle East said in recent interviews. The officials said Islamic fund-raisers have taken donor files and moved from one group to another a step ahead of the authorities, officials said.

Islamic charities became a major focus after the Sept. 11, 2001, terrorist attacks, when U.S. officials concluded the charities played a large role in sustaining the infrastructure of radical Islamic groups. Using a set of new laws, the U.S. Treasury froze the assets of numerous groups in the U.S. and overseas.

But over the last six years little evidence has emerged directly connecting charities to individual acts of terrorism, and Muslim leaders and civil libertarians have charged that the government is over-reaching in pursuing the charities.

Questions about the government's approach arose particularly after prosecutors failed in some high-profile trials to prove that charities were connected to terrorists or terrorist organizations. The charities' leaders and their supporters say they send money from American Muslims to legitimate social and aid organizations in the Middle East.

One scholar, Ibrahim Warde of the Fletcher School of Law and Diplomacy, argues in a 2007 book, "The Price of Fear," that the connection between charities and terrorism is largely a myth.

Government officials, while acknowledging that charities' role in individual attacks seems to be slight, say evidence from several of the criminal cases have demonstrated direct ties between charities and terrorist groups, including al Qaeda and its affiliates.

Kenneth Wainstein, the Justice Department national-security chief, said in an interview that intelligence reports continue to find that charities are being used by terrorist groups to provide both funds and logistics help, such as with visas and work permits in conflict zones. Mr. Wainstein and other officials say many of an estimated six million Muslims in the U.S. follow the tenets of their faith and give generously to charities that promote Islam and provide welfare to needy Muslims in places like Afghanistan and Iraq, but the funds often are diverted to other purposes in these war zones to underwrite items such as communications, logistics and medicine for groups fighting the U.S. military or U.S. allies.

In the years after Sept. 11, the Justice Department now alleges, fund-raising efforts in the U.S. shifted to at least two existing groups that were missed in the initial sweep: a charity in Boston called Care International, and another in Columbia, Mo., called the Islamic American Relief Agency. Care International's officers were recently convicted of tax fraud in Boston federal court, while backers of the Missouri group are under indictment for similar offenses. In the Care International case, prosecutors presented evidence that the group was an extension of Osama bin Laden's original outpost in the U.S., a Brooklyn-based Islamic organization. But Mr. Warde criticized prosecutors for not charging any of the defendants with terrorism support. The Care International officers are expected to appeal.

A month after the government shut down many top charities in December 2001, Islamic fund-raisers set up a new group in Toledo, Ohio, called Kindhearts, which the Treasury in 2006 shut down and identified in a public statement as "the progeny of Holy Land Foundation and Global Relief Foundation," two defunct charities that the U.S. designated as supporters of terrorism. Two other charities, Kinder USA and Life for Relief and Development, remain under investigation but have denied any ties to terrorism.

Terrorism investigators say Islamic charity fund-raisers are more sophisticated than they originally realized. Khalil Jassemm, the founder of one group under investigation, self-published a 494-page guide to running such groups -- "Islamic Perspective on Charity, a Comprehensive Guide for Running a Muslim Nonprofit In the U.S." -- that walks charity officials through the numerous laws governing such groups. The book was made available by The Investigative Project, a Washington nonprofit that researches terrorism issues.

Mr. Jassemm founded Life for Relief and Development. Terrorism investigators say some of its personnel are supporters of the Islamic Party of Iraq and in 2006 was raided by the FBI in Michigan and by the U.S. military in Iraq. A spokesman for the charity said Mr. Jassemm has left the group and now lives in Jordan. He didn't respond to an email request for a meeting. The group says it isn't affiliated with any political groups in Iraq.

Officials say the moves against the organizations have aroused anger and opposition among many American Muslims and some civil-liberties advocates -- creating what counterterrorism officials acknowledge is a public-relations problem.

For one thing, critics have chided the government for keeping much of its evidence of terrorist connections secret and resorting to nonterrorism charges, such as tax and money-laundering violations, to put the leaders of some charities out of business.

Prosecutors say, though, that they won't abandon tactics that have brought results. "We incapacitate the bad guys," said Justice's Mr. Wainstein. "It might not be the sexiest way of doing it, and if we get criticized, so be it."

One big problem, some front-line prosecutors said, is that intelligence can show signs of terrorism support, but it is difficult to obtain the kind of unambiguous evidence that will stand up in court to prove money ended up with terrorists overseas. "Once it hits a foreign bank, it is gone to us," said one federal prosecutor who asked not to be named.

• The News: Counterterrorism officials who shut down Islamic charities that they accused of funding terrorist organizations are targeting a second group of charities.
• The Background: Officials say Islamic fund-raisers have taken donor files and moved from one group to another, remaining a step ahead of authorities.
• The Controversy: Over the last six years, little evidence has emerged directly connecting charities to individual acts of terrorism."Government can come in and close down the charity, but the donor list still exists," said prosecutor Pat Roane, the Justice Department's point man on terrorism financing. "The donor list is gold."

Write to Glenn R. Simpson at glenn.simpson@wsj.com