23-year-old Bernal missed last month's Critérium du Dauphiné due to a back issue, but finished among the 16 group of favourites on Stage 4 - the first summit finish of this year's Tour de France - on Wednesday (AEST).
However, during a relatively quite Stage 6 on Friday (AEST), Bernal's teammate Kwiatkowski opened up in pursuit of Julian Alaphilippe before looking back at the Colombian.
Mollema has since claimed that when he rode past Bernal and Kwiatkowski to close in on Alaphilippe, the 2019 Tour de France winner ordered the lowering of their team's pace.
"I was a bit surprised that Bernal had to leave a gap," Mollema told NOS.
“He said 'easy easy' to Kwiatkowski in the last 200 meters.
"Maybe he didn't want to go any faster or he didn't feel well."
Meanwhile, Bernal hit back at such claims, saying patience and recovering is key after he placed eighth on Stage 6.
"I'm feeling a bit better every day and today I felt much better. We have to remain patient and recover as well as possible," Bernal said, according to El Tiempo.
"It was a pretty hard day, and we're going to feel it in the legs. The final climb was hard, so there were no attacks.
"It's one of those days that will be felt in the legs the following day and adds to the accumulated fatigue in the final week."
The Tour de France continues with the 168km seventh stage from Millau to Lavaur which should be one for the sprinters but might entice the opportunists.
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