"They have got to look for alternative land," the Reuters new agency reported Maria Mutagamba, Uganda's environment minister, as saying.
He said the National Forest Authority (NFA) had blocked the license.
Yoweri Museveni, Uganda's president, has faced intense opposition over proposals to grant private firms rights to bulldoze protected forests areas.
Three people died in protests in April against government plans to give 7,100 hectares of the Mabira Forest, a nature reserve since 1932, to a private sugar producer.
Last year two NFA board members and Olav Bjella, the group's executive director, resigned in protest over the granting of a license to Bidco to bulldoze parts of the Kalangala Forest.
Isaac Kapalaga, an NFA technical director, also resigned, having reportedly been pressured into granting Bidco its license.
A number of environmental organisations had also been seeking court orders to prevent the government from handing areas of rainforest over to private companies.
Marked for development
Like the Mabira Forest, Bugala island, which had been marked for development by Bidco, is home to rare species of plants, animals and birds.
"The government is supposed to give us land. We signed, so we are waiting for that land"
Kodey Rao, Bidco Uganda director
But Kodey Rao, Bidco Uganda's director, said the company was not interested in taking forest reserves.
"We never asked for the reserves," he said. "The government is supposed to give us land. We signed, so we are waiting for that land."
Bidco, which specialises in edible oils, has already planted 4,000 hectares of oil-providing Malaysian palm trees on Bugala, mostly on land from which non-protected rainforest was bulldozed.
The company says it requires a further 2,500 hectares. A private letter from Mutagamba to the cabinet in January said that Bidco was concerned the project would "jeopardise the loans they were processing with ... financing agencies due to ... negative publicity."
Palm oil crops have been hailed as a new biofuel, helping to help reduce dependence on fossil fuels and fight global warming.
But environmental groups say that big palm oil firms are clearing millions of hectares of carbon-storing rainforest to make way for their plantations.