It is another blow to the country's reputation for dealing with livestock following international criticism in 2011 when the ABC's Four Corners program aired footage of Indonesian abattoir workers torturing cows shipped from Australia.
The scandal prompted the Government to suspend live exports to Indonesia for a month.
In the latest pictures, taken by an AFP photographer, a crane is shown transferring three bony cows from a boat in the eastern Javanese city of Surabaya using a loop of rope around their skulls.
Another photograph shows seven live cows being lifted in a similar fashion in one group, with their necks outstretched.
The boat transporting the cattle had come from Sumbawa island, around 500 kilometres east of Surabaya, but it is not clear whether that is where the cattle were reared.
The cattle were to be transported to the capital Jakarta, according to a worker in the operation who declined to give his name.
It is not known which company was transporting the cattle.
While a large number of cattle are transported around Indonesia, an archipelago of more than 17,000 islands, it is not normal practice to lift animals up by their heads.
"It is crazy that cruel practices are still happening," Jakarta Animal Aid Network campaigner Benvika told AFP.
Indonesian Veterinary Association chairwoman Wiwiek Bagja said animal welfare laws in effect since 2009 did not work because they do not actually lay out what punishments people should face for animal cruelty.
"In short, Indonesia is very far from implementing and enforcing the law," she said.