Brisbane water police are searching central Moreton Bay for a missing tinnie after two men on board failed to return home.

Police said the pair, aged 31 and 25, called family to tell them they were coming back from their fishing trip near the Port of Brisbane at 10:15pm on Saturday but never arrived.

Their car and boat trailer were still parked at the Whyte Island Boat Ramp.

The missing boat was described as a dark blue, aluminium tinnie.

It is 3.3 metres in length with a red Queensland registration number on the side reading OM209Q.

Both men are from Brisbane.

Carwyn Massey has been missing since Saturday night. ( Instagram )

The sister of one of the men, Rhiannon Massey, took to social media in a desperate call to find her brother.

"My brother Carwyn Massey has been missing since last night," she said.

"If anyone hears anything please contact the police or myself and my family."

Rough, windy conditions increase difficulty of search

Inspector Karl Hahne said the men set out on a fishing trip on Saturday but police were unsure exactly where they were fishing within Moreton Bay.

He said windy conditions added to the already difficult large-scale search.

"The weather conditions today have been very poor," he said.

"The water temperature is between 20 and 23 degrees, the swell is as high as 1.5 metres so very rough conditions not only for the missing men but the searchers.

"It's a very large search area.

"With these windy conditions the men, if they are in the water, could float a long way."

Inspector Hahne said there were 13 police and coast guard boats involved in the search effort as well as several helicopters being coordinated from Canberra.

"[The families of the men are] holding out hope that the search is a success, as we are," he said.

"They're very distressed."

Police are searching the waters around Moreton Bay as well as islands in the area including Moreton and Stradbroke Islands.

Inspector Hahne said conditions were difficult even for large police vessels, and the search would go until last light.

"This wind will probably persist until early tomorrow morning, maybe as late as 9:00am or 10:00am so the conditions aren't going to get any better in the short term."