But the move comes as councillors decide tonight whether to press ahead with cuts totalling£1m that could lead to 400 job losses.
An independent review conducted for the council found that 11 chief officers were being paid£17,000 less than the national average.
A council spokeswoman said: 'In October 1998 the Joint National Council for Chief Officers concluded a 3% pay award for chief officers which Sefton and other authorities were contractually required to implement.
'The national average is£62,610 and the majority of our service directors are on approximately£45,000.'
A report on directors' pay went to a cabinet meeting on 28 October but a decision has been deferred until 28 November. The spokeswoman added: 'There are no figures in the public arena to state how much the structures are being changed.'
Nigel Flannigan, Unison branch convenor, said big pay rises for senior staff would be 'obscene and criminal'.
'People on the lowest wages on the council are being told their jobs may not be there but on the other hand they're discussing awarding pay rises to chief officers, including the chief officers who are proposing the redundancies,' he said.