The low frequency rumble of ship engines as they pass through the Great Barrier Reef could affect whales’ ability to communicate, researchers say.

Ships passing through the Great Barrier Reef could disrupt whales’ ability to call out to one another, a study has found.

Researchers from James Cook University used a large underwater microphone to record noises at a reef off Townsville for three months last year.

Professor Colin Simpfendorf, who recently analysed the recordings, said three main sounds could be heard.

These were general weather-related background noises, whale calls and marine life sounds and the rumble of ship engines.

“The [low frequency] noise created by the vessels is about the same of that used by whales to communicate,” he told AAP.

Prof Simpfendorf says as the research is only in its early stages he can’t be sure what effect engine sounds have on whales.

“But one of the things we’ve wanted to highlight is that increasing traffic may in the future lead to concerns,” he said.

He said if the noises got significantly louder they could disrupt the whales’ ability to communicate over long distances and mask their calls.

“They use the sound to co-ordinate family groups, communicate with calves, those sorts of things,” he said.

Jill Perry, who has run tour firm Hervey Bay Whale Watch for almost three decades, said boat engines didn’t seem to affect the mammals.

“The engines of the boats seem to attract the whales because I think they know they’re not in any danger [while they're in Hervey Bay],” he told AAP.

Prof Simpfendorf said little research had been carried out on how ship noises affected whales and he was hopeful funding would be put aside to better understand potential issues.

Last year the United Nation’s environment arm raised concerns about possible effects the number of developments along the Queensland coast may be having on the reef.

Comment has been sought from the Great Barrier Reef Marine Park Authority.