Cardinal Peter Appiah Turkson, a Ghanian who heads the Vatican's office for justice and peace, likened such economic dependence on big corporations to a new form of slavery.
It was the second time in a month that the Vatican has made clear that while it's not entirely opposed to biotech foods, it is firmly not in favor of them, either.
The United States, home to major multinationals that produce biotech seeds and crops, has lobbied the Vatican for years to persuade it to speak positively about genetically modified organisms, calling biotech a "moral imperative" to feed the world's hungry.
And for years Turkson's predecessor, Italian Cardinal Renato Martino, obliged, touting the benefits and safety of GMOs and even hosting a biotech conference at the Vatican in 2003.
But Turkson reversed course in an interview Tuesday with the Vatican newspaper L'Osservatore Romano.
While saying he personally wasn't for or against GMOs, Turkson said the key issue concerned giving farmers access to suitable land that hasn't been eroded by multinational logging or mining companies.
"As a result, you wouldn't need any genetic engineering," Turkson told the paper. "In this way, the farmer wouldn't have to buy GMOs from abroad. I ask myself, why force an African farmer to buy seeds produced in other lands and with other means? The doubt arises that behind this is the play of maintaining economic dependence at all cost."
"I'd even say it becomes like a new form of slavery," he added.
Last month, the Vatican spokesman Rev. Federico Lombardi put out a statement about GMOs after Italian news agencies erroneously reported that the Vatican had come out in favor of them during a conference.
The conference was held at the Vatican's Pontifical Academy of Sciences and its final paper was favorable to GM crops. But Lombardi noted that only seven of the 40 scholars who attended were academy members. As a result, he said, the final statement was not an official position of the academy or the Holy See.
The Vatican's position on GMOs has been carefully watched, given the moral weight of its positions concerning combatting poverty and hunger. U.S. cables from the WikiLeaks trove of documents illustrate how critical the Vatican's position was - and how the U.S. tried to sway it in light of resistance from some parts of the Catholic Church.
One cable concluded that there was "cautious acceptance" of biotech food by the Holy See but that economic dependence was a major concern, particularly for Catholics in the developing world, and that regardless the Vatican wouldn't challenge individual bishops who opposed them.
Washington's greatest ally in the lobbying effort was Martino, who would frequently refer to all the GMOs he safely ate while living in New York as the Vatican's ambassador to the U.N. But the cables indicate Martino may have merely been playing a good diplomat.
"A Martino deputy told us recently that the cardinal had cooperated with (the embassy) on biotech over the past two years in part to compensate for his vocal disapproval of the Iraq war and its aftermath - to keep relations with the US (government) smooth," according to one cable.
"According to our source, Martino no longer feels the need to take this approach," the cable said.
The Vatican has said the WikiLeaks cables reflect only the views of the people who wrote them and are not official Vatican positions.