Having made the step up from the World Supersport series to World Superbikes at the start of this year, the Dutchman has impressed with the Pata Honda team and he secured his maiden podiums at Assen in the middle of April.
With Karel Abraham ruled out of last week's MotoGP event in the Netherlands with a foot injury, it was reported that Van der Mark would take the Czech rider's place at AB Motoracing.
However, he failed to make the grid.
"I think there was a big misunderstanding. It was the team’s decision," he told worldsbk.com.
"It’s all about budget. HRC (Honda Racing Corporation), Honda Europe and my team agreed with me that I would ride at the weekend, but the team decided not to take any risks about crashing, so I couldn’t do anything about it."
Asked if you could make his debut later this year, he replied: "I’m available."
He added: "I’m a young rider. I think every young rider has a dream to get into MotoGP. We will see what happens. If there is a good possibility, I will go. If not, I will stay in World Superbike because I enjoy it here."