The Latics chairman was clearly unhappy with what he saw in the defeat to Swansea City and this is the first public message from the chairman against the manager.
Speaking to BBC Radio 5 Live, Whelan said: "That was our worst performance in four or five years.
"I will have a meeting with him on Monday morning and ask him some questions about the performance and his selection.
"We had three quality players on the bench and I want to know why."
What Whelan did reveal was that the future for Martinez is secure and his job is not on the line.
"Roberto Martinez's future is secure. He has done a great job for the club," added Whelan.
"But we will have a meeting on Monday when he will put his cards on the table and I will do the same."
It is expected that Whelan we will explain to Martinez that Diame and Rodallega, two players set to leave the club in the summer, cannot be isolated from the first team.