“Lock them all down,” Trump said as chants rang out around the event in Muskegon, Michigan.
Members of the militia are accused of monitoring his vacation home in northern Michigan and exploring a nearby bridge to plant a bomb.
Authorities say the group was also targeting law enforcement officials in the state for an attack ahead of election day.
“I guess they said she was threatened and she blamed me, she blamed me and it is our people working with her people, so let’s see what happens,” said Mr. Trump as the crowd chanted “Lock her up” for a second time.
“Our FBI needs to start looking at the antifa and the people they don’t look at the way they should be.”
Mr Trump then said: “Hope you send it soon anyway.” “
A member of Ms Whitmer’s staff took to Twitter to criticize the president’s attack.
“I am the governor’s deputy digital director. I see everything that is said about her and her online, ”said Tori Saylor.
“Anytime the president does this at a rally, the violent rhetoric against him immediately escalates on social media.
“It has to stop. It just has to stop.
Previously, the president had laughed as the crowd chanted to him to stay “12 more years.”
“It drives them crazy when you say ’12 years older’. Then they say, ‘He’s a fascist, he’s a fascist,’ Mr Trump said as the crowd sang him.