Carter, whose organisation, the Carter Centre, filed a "friend of the court" brief in the case, said in a statement, "We are disappointed that the Supreme Court has upheld a law that inhibits the work of human rights and conflict resolution groups."
"The vague language of the law leaves us wondering if we will be prosecuted for our work to promote peace and freedom," he added.
Carter joined numerous civil and human rights advocates in attacking the court's 6-3 ruling "to criminalise speech" in Holder v. Humanitarian Law Project. It was the first case to challenge the Patriot Act before the highest court in the land, and the first post-9/11 case to pit free speech guarantees against national security claims.
Chief Justice John Roberts wrote for the court's majority, affirming in part, reversing in part, and remanding the case back to the lower court for review.
Justice Stephen Breyer dissented and read his dissent aloud before his fellow justices - always a sign of an opinion very deeply felt. He was joined by Justices Ruth Bader Ginsburg and Sonia Sotomayor.
Plaintiffs sought to provide assistance and education on human rights advocacy and peacemaking to the Kurdistan Workers' Party in Turkey, a designated terrorist organisation. Multiple lower court rulings had found the statute unconstitutionally vague.
The plaintiffs' lead lawyer, Georgetown Law Centre's David Cole, a widely respected constitutional scholar, sees the "material support" paradigm of "preemptively weeding out threats to national security, guilt by association" resurrected from the McCarthy era.
He told IPS, "While it was illegal in the 1950s to be a member of the Communist Party, it is now a crime to support an individual or organisation on a terror watch list, although the government can designate and freeze assets without a showing of actual ties to terrorism or illegal acts."
Cole asserts that support for the lawful activities of a designated group should not be unlawful, and that the not- for-profit sector needs to insist that constitutional rights apply in the war on terror. He is calling for changes in the enabling legislation when Congress returns from its August recess.
"While the House Un-American Activities Committee once relied on the private sector to mete out punishment through the destruction of reputations and careers, today measures such as the Anti-Terrorist Financing Guidelines have turned funders into the new enforcers. In this light, he said the nonprofit sector has an obligation to resist such a partnership with government," he says.
Instead, the court found that the statute did criminalise speech on the basis of its content, but then found that the government's interest in delegitimising groups on the designated "terrorist organisation" list was sufficiently great to overcome the heightened level of scrutiny.
This one of a very few times that the Supreme Court has upheld a criminal prohibition of speech under strict scrutiny, and the first time it has permitted the government to make it a crime to advocate lawful, nonviolent activity.