Two men have been rescued after a boat struck a log and drifted up to 50km on the Waikato River.

The stricken vessel drifted for nearly three hours until rescuers spotted it about 5.45am.

A police spokeswoman said the pair were in their motorboat about 3am when it hit a snag and started taking on water between Ngaruawahia and Huntly.

Without oars and a broken-down motor, the stricken vessel started drifting towards Mercer, swept north by the strong current and no means of controlling where it went.

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One of the men decided to abandon the vessel, swimming to shore to raise the alarm.

The second man remained on board and with his torch tried to show rescuers his ever-changing position. He also described to police over his cellphone key bridges as he passed under them.

"The guy left with the boat was trying to figure out where he was," said the spokeswoman.

"He had a torch and was flashing it and trying to figure out what bridges they were between."

Eventually the foundering craft was found near Mercer, 52km from Ngaruawahia, and police and fire boats rescued the man.

A police spokesman said it was not clear why the pair were on the river in the first place but both men were safe.