Police Scotland said: “The body of one of the men has been recovered, however formal identification is yet to take place.
“The next of kin of the men are aware and are being supported by officers.
“Extensive searches, assisted by HM Coastguard and RNLI, are ongoing.”
The RNLI said Stornoway’s all-weather lifeboat was launched at 21:42 on Tuesday to search for the overdue fishing boat.
A spokesperson added: “The search, involving coastguard air and ground assets, was joined by Lochinver RNLI’s all-weather lifeboat a short time later and continued into Wednesday morning.”
The search has come during warnings of bad weather in the area.
A weather system containing the remnants of Hurricane Isaias is forecast to send gales, heavy rain and a surge of warm air to parts of the UK.
A Met Office yellow warning has been issued for parts of the Highlands and Western Isles with the risk of gusts touching 70mph (113km/h) in places.