England boss Jones has featured regularly in the media during his side's tour Down Under this summer, whereas Cheika has refused to criticise the visitors or Jones, with whom he played at Randwick.
England have dominated on the field, clinching their first-ever series victory in Australia with a 23-7 win in Melbourne on Saturday, and Hansen believes that the media antics of Jones have had an influence in the games.
"Cheika's not come back, he's letting Eddie have a free rein - to the point where it actually seems like he's letting Eddie bully him in the media," the World Cup-winning boss told reporters.
"I don't know if that's because they know each other that well, or if there's a pecking order from the old days. That's gone on to the park, hasn't it?"
England will look to complete an unprecedented series whitewash in Australia when they meet for the third Test on Saturday.