American scientists have reacted with anger at a court ruling that strikes down Barack Obama's decision to greatly expand medical research using stem cells taken from human embryos.

Scientists described the order by a federal judge in Washington, who said that the president had overstepped a law barring the government funding of research in which human embryos are destroyed, as "deplorable" and "a serious setback" in the search for cures to major diseases.

Lawyers for an alliance of Christian groups who brought the case, which tied opposition to experiments on embryonic stem cells to the anti-abortion campaign, said the ruling appeared to go further than restrictions under President George Bush and bar all government funding for such research. It also pushes the ever-contentious issue of abortion to the fore again in the runup to November's mid-term elections and presents Obama with the difficult choice of whether he wants a battle in the courts and in Congress to repeal the legislation.

The court order came after an executive order by Obama in March last year that lifted restrictions put in place by Bush eight years earlier. Those restrictions limited government funding to a small number of existing lines of human embryonic stem cells. The administration had allocated about $250m (£160m) to the research. The National Institutes of Health added an additional 70 lines after Obama's order. But Judge Royce Lamberth ruled that the president's decision was in conflict with the Dickey-Wicker amendment, a 1996 law that bars the use of government funds for "research in which a human embryo or embryos are destroyed". The law has been renewed by Congress each year.

Scientists swiftly condemned the ruling. The California Institute for Regenerative Medicine (Cirm) said the court order would disrupt advances in research for cures to diseases such as diabetes and Lou Gehrig's. "The decision is a deplorable brake on all stem cell research," said Cirm's president, Alan Trounson. "Many discoveries with other cell types ... would not happen without ongoing research in human embryonic stem cells."

Steven Aden, a lawyer for the Alliance Defence Fund which brought the case, said: "We're gratified that the court accepted what we think is a plain and commonsense reading of the applicable law and we're hopeful that ultimately this will result in the renewal of good, science-based funding for adult stem cell research."

Scientists were also left confused over whether they had to immediately halt embryonic stem cell work paid for with government funds or if the ruling only prevented federal authorities from distributing more grants.

Cirm said the order appeared to bar research permitted even under the tighter regulations imposed by Bush.

Aden said he believed the ruling prohibits any government-funded research involving embryonic stem cells.

"We think that's right. When congress passed the Dickey-Wicker amendment back in the days of the Clinton administration the reason for that was to get the American public out of funding research that involves the destruction of human life," he said.

An opinion poll by the Pew foundation last year found that 54% of Americans support research using human embryos.