The discovery, made by a team of US scientists sailing on a US Navy research vessel, will add to the concern that the din now being made by humans in the oceans could be having a detrimental effect on marine life.
The team transmitted 10, 42-second, low-frequency active (LFA) sonar signals at 16 humpbacks.
The whales' songs, which are thought to be mating calls, were about 30% longer than normal during the broadcasts.
Notes, phrases and themes
Patrick Miller, of the Woods Hole Oceanographic Institution (WHOI), Massachusetts, US, told the BBC: "If whales are exposed to these types of sounds over long periods during the breeding season, there is a chance that they could interfere with the animals' mating system and perhaps the outcome of actual mating events."
During the breeding season, male humpbacks will sing long, complex songs that contain several "themes" that progress in a predictable order.
"Each sound you hear is a note, and they combine notes into phrases, and then phrases into themes, and themes add up to be a song," Patrick Millar said. The songs will last typically 10 to 15 minutes.
During the sonar transmissions, however, the songs, whilst keeping the same structure, got considerably longer.
Hearing damage
The WHOI researcher said the results were very strong given the low power used in the tests.
Sonar, propellers, seismic surveys, sea-floor drilling, and low-frequency radio transmissions have all turned the oceans into a noisy place. There has been concern for some years now that man-made sounds could make it much harder for whales, dolphins and other sophisticated marine animals to communicate, navigate and even detect predators and prey.
"Animals that are particularly close to sonar when it broadcasts are exposed to very high levels of sound and could have actual hearing damage or some sort of physical trauma," Patrick Miller said.
"Animals spread over a much larger body of water could be exposed to lower levels of the sound but those levels may still cause behavioural responses."
The research is published in the journal Nature.