The galvanised steel structure at St Tudwal's Island West, near Abersoch, is designed to hold two rib-type boats.
Gwynedd's area of outstanding natural beauty (AONB) unit fear it will visually impact on the area.
But local councillors approved the plan at a meeting on Monday on the recommendation of planners.
TV explorer Mr Grylls, 41, bought the island for ??95,000 in 2001. In 2013, he had to remove a slide that ran into the sea after facing a planning investigation over its erection.
As well as holding the boats, the structure he has gained permission for is designed to cope with an expected 3ft (0.9m) rise in sea levels over the next century.
A Gwynedd AONB spokesman said it would "disturb the area's tranquillity", with dolphins and seals populating the waters.
Sections of the slipway will be under water at certain times, depending on the tide, and it will be painted grey to try and blend in with rocks.
Gwynedd council planners took this into account and a spokesman said ahead of the meeting: "It is considered that the proposal would not cause significant harm to the landscape or the seascape."
Adventurer Bear Grylls has gained council approval for a 129ft (39.3m) slipway at his Gwynedd retreat despite opposition.