WASHINGTON — The Senate is seeking to reverse a controversial law that allows farmers to harvest genetically modified crops even when the crops are caught up in legal battles.

The law, passed as part of a spending bill earlier this year, has become a flashpoint in the national debate over genetically engineered foods. It would expire at the end of the federal budget year next week, and a temporary spending bill passed by the House would extend it. But Senate Democrats’ spending bill would let it expire.

The narrow provision only applies to genetically modified crops that are under litigation. It allows the agriculture secretary to grant permits for farmers to continue to grow engineered crops while appeals are pending, even if courts have ruled that the Department of Agriculture shouldn’t have approved them.

The provision’s supporters say it is designed to help farmers weather the sometimes yearslong appeals process and avoid stops and starts in planting as courts reverse each other’s decisions. Genetically modified seeds, especially those engineered by seed giant Monsanto, have been the subject of several lawsuits by environmentalists in recent years, often putting farmers who use them in a bind.

Monsanto and several major farm groups backed the provision, and it soon became a rallying point for activists who oppose genetically engineered crops. They dubbed it the “Monsanto Protection Act,” a title that stuck and was even used by Democratic opponents of the measure on the Senate floor.

“It raises profound questions about the constitutional separation of powers and the ability of our courts to hold agencies accountable to the law and their responsibilities,” Sen. Jeff Merkley, D-Ore., said during debate over a wide-ranging farm bill last summer. “This process and this policy has provoked outrage across the country.”

Agriculture Secretary Tom Vilsack similarly questioned the proposal, saying he believes that he already has the power the law gives him. Referring to the backlash against the provision, he said in May that the law created confusion and suggested that it made it harder to find compromise between advocates and opponents of genetically modified crops, an effort that Vilsack has made a priority in recent years.

“It makes that conversation just a bit more difficult than it has to be,” he said then. “Why stir up the pot if you don’t have to?”

Genetically modified crops, often grown from seeds engineered by Monsanto and other companies to resist pesticides and insecticides, have grown exponentially in the last two decades and now represent a majority of many crops, including corn and soybeans. While mainstream science hasn’t uncovered any dangers, opponents say the foods haven’t been studied enough to fully understand the long-term effects.

Though Monsanto continued to support the provision — it spent more than $3.5 million to lobby on the spending bills and other issues in the first half of this year — support in Congress for the provision appeared to wane after Vilsack made his case. An agriculture spending bill approved by the House Appropriations Committee in June would not have extended it.

The temporary spending bill passed by the House last week, designed to avert a government shutdown, would have extended the provision because it did not explicitly add language to reverse it. House leaders so far haven’t objected, though, to the Senate provision on the genetically modified crops, though the fate of the larger spending bill is unclear.

As opponents have rallied, few lawmakers have stood up to defend the provision. Republican Sen. Roy Blunt of Missouri, where Monsanto is based, took a lonely stand on the Senate floor this summer to counter his colleague Merkley.

“The only people protected here are the people who have put the seeds in the ground,” Blunt said, saying opponents had exaggerated its effects.

In an unattributed blog post this week, Monsanto said that the provision’s potential expiration was “no surprise” but that it was necessary to help farmers weather a number of lawsuits against genetically modified crops filed by opponents.

“Its purpose was to reinforce the integrity of the regulatory system and protect farmers from the disruption of frivolous lawsuits,” the company said, adding that it “was needed to offset the impact of a small, well-funded group of special interest activist groups using the legal system to try and block growers from having access to biotechnology, period.”