A spokesman said the Western Isles Presbytery was taking the allegations against the late Reverend Dr Iain D Campbell "very seriously".
The allegations are understood to relate to Dr Campbell's personal life.
The minister of Point Free Church on Lewis died at the end of January, aged 53.

The referendum will take place on 10 March, but Bath Conservative MP Ben Howlett said he was concerned about a "lack of awareness" about the issue.
Mr Howlett also said he is worried about the public's level of engagement.
Bath and North East Somerset Council said the referendum had been publicised in press releases and tweets.
It also said it was the subject of a two-page article in the winter edition of the council magazine which was distributed to all households in the region.
A further news release and polling cards will also be sent out to all households this week, the authority added.
Supporters of the referendum say Bath needs a mayor to give local government more visibility.
Directly elected mayors were created by the Local Government Act 2000 as one option for local government, as long as the idea was backed in a referendum.
Mr Howlett said he was "personally concerned" that an elected mayor was not appropriate for an area "as diverse" as Bath and North East Somerset, and that it could "lead to an increase in the cost of local politics".
"The level of misinformation on this issue is worrying - many people seem to still believe this is about a mayor of Bath and not understanding it would cover all of Bath and North East Somerset.
"I hope in the coming weeks more information will be forthcoming to enable residents to make an informed decision," he added.
The Free Church of Scotland is investigating allegations made in connection with a minister on the Isle of Lewis who died earlier this year.
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An MP has criticised "the level of misinformation" about a referendum on an elected mayor for Bath and North East Somerset.