Millwall have been looking for a new boss since Kenny Jackett quit at the end of the season in search of a fresh challenge after six years at the Den.
He has since taken over at Wolves and former West Ham midfielder Lomas is long odds-on to replace him with reports claiming he has flown to Portugal for talks with Lions chief executive Andy Ambler.
In a statement, Saints chairman Steve Brown said: "I have been contacted by Millwall and following discussions have given them consent to speak to Steve.
"He is an ambitious and talented manager and I'm disappointed but not surprised that his progress has been monitored by other clubs.
"As with our previous two managers, we will not stand in the way of Steve if he agrees to join Millwall."
St Johnstone is Lomas' first job in management having joined them in November 2011, winning 26 out of 72 games and leading them to a third-place finish in the SPL last season.
Should the former Northern Ireland international take up the Millwall post, current St Johnstone assistant Tommy Wright is favourite to succeed him at McDiarmid Park.