The Royal Navy frigate HMS Somerset is due at its home port, days after its captain was ordered back to the UK.
Commander Axon is facing complaints from two crew members
Commander David Axon was relieved of his command at the weekend to face an internal inquiry into complaints from two crew members about his leadership.
Defence officials said the "highly unusual" move followed an "equal opportunities investigation".
HMS Somerset is returning to Plymouth's Devonport dockyard after six months in the Gulf protecting Iraq oil platforms.
It is expected back in port under the command of the vessel's executive officer sometime after 0800 GMT on Thursday.
Cdr Axon was relieved of his command when the ship reached Gibraltar.
It was initially thought a junior officer's claims of bullying and intimidation on board the vessel had prompted the move.
But the Ministry of Defence has now confirmed that both the male officer and a female crew member had made separate complaints of a similar nature against Cdr Axon.
A spokesman for the MoD said: "We can categorically deny that the allegations were of a racial, sexual or violent nature."
HMS Somerset has been protecting Iraqi oil platforms
The ministry said the decision to recall Cdr Axon to the UK had been taken because it was "in the interests of all the people concerned".
"A ship is a small community," a spokesman said. "It was entirely appropriate for Cdr Axon to be given time to consider the allegations away from the ship."
BBC west of England correspondent Jon Kay said it was understood the commander had now given his version of events to an internal inquiry, which could report its findings within days.
Cdr Axon, who is in his 40s and lives in Southsea, Portsmouth, has so far not made any public comment on the allegations.
Although no decision on his future has been taken, if he is cleared he could be reinstated.
The MoD said earlier in the week: "The Royal Navy is an equal opportunities employer and is proud of its record.
"The service takes all such matters very seriously and acts swiftly to resolve issues of this nature when they are reported.
"At this point, no decision on the CO's future has been taken."