Pique backed the referendum, which had been declared 'illegal' by the country's central government, and accused Spanish authorities of making things worse in terms of Catalan separatism by how things were handled.
He even likened it to the era of oppression under former Spanish dictator General Franco.
"You vote yes, no, or leave it blank, but you vote. In the Franco era, we couldn't defend our ideas," the World Cup winning centre-back had said in the wake of the interrupted voting process.
"I am, and I feel Catalan, and I am very proud of the people, of their behaviour."
23 mins of training and Spain are done. Piqué goes off with security guard, objects thrown. What a mess…https://t.co/dWYrzTTOwd— David Cartlidge (@davidjaca) October 2, 2017
Pique has been careful not to come out publicly on one side of the other, but even just his support of the right for Catalans to vote has drawn criticism from plenty in Spain.
He was greeted by a chorus of boos and jeers from the stands when he made his way out onto the training pitch, with a number of fans holding signs and placards which read, 'Pique Fora' - translated to Pique Out.
The session was then quickly wrapped up after barely 20 minutes.
Also on Monday, the 30-year-old said that he would be willing to step down and withdraw himself from the national team ahead of next summer's World Cup if his continued involvement while he supports the referendum is seen to be disruptive.
In his own mind, he want to keep representing Spain, but won't if it causes problems.
"I think I can continue.
"But if the board really thinks I'm a problem, I will take a step back and leave the national team before 2018," he said.