Biologists and villagers in a remote corner of the Amazon rainforest were searching for a 12-tonne whale yesterday that had reportedly lost its way and become stranded 1,000 miles from the ocean.

The five-metre long (16ft) creature, which biologists said was probably a minke whale, became stranded on a beach on the Tapajos river, 39 miles from the city of Santarem. Environmental experts said the whale had probably become separated from its group in the Atlantic Ocean, off northern Brazil, after falling ill or being hit by a boat.

The whale appeared to have entered the Amazon near the city of Belem before reaching the Tapajos, a tributary of the Amazon. Efforts to rescue the animal began on Tuesday, after local fishermen contacted environmental officials in Santarem by radio. On Thursday biologists arrived at the scene by boat and isolated the sandbank.

Residents of Piquiatuba, an isolated settlement of about 70 families in the Amazon state of Para, also helped to try and free their unexpected visitor, splashing water onto its skin to protect it from the scorching sun. Images broadcast on Brazilian television showed dozens of fishermen and curious locals crowded together in the river around the whale's large grey fin.

On Thursday night after rescuers managed to free the whale it disappeared into the waters. Environmentalists used helicopters and boats to try and find the whale, without success.

"What we can definitely say is that it lost its way," Fabia Luna, a government biologist involved in the rescue, told Globo television. "It entered the river, which on its own is unusual. But then to have travelled around 1,500km is both strange and adverse."

"It is very atypical [to find] a whale in Amazonia," Katia Groch, a whale expert from the Instituto Baleia Jubarte (humpback whale institute), told the Folha de Sao Paulo newspaper. "It may have lost its way, perhaps because of illness. We will only know when we can examine it."

Although the whale's presence was only confirmed this week, Daniel Cohenca, the regional head of Ibama, Brazil's environmental agency, said it may have been in the region for up to two months.

In recent weeks residents near the Tapajos river are said to have become alarmed at the presence of an unidentified animal. Some locals had ordered their children not to swim in the river after rumours spread that a "big cobra" had been spotted.

"There are people who just don't understand how this kind of animal survived in fresh water," said Cohenca.

Rescuers fear that, alone, the whale will have difficulty returning to the Atlantic.

"It is outside of its normal habitat, in a strange situation, under stress and far from the ocean," said Groch. "The probability of survival is low."