The Danish company's vice-chairman Kirk Kristiansen told the Wall Street Journal the decision was made in the consumer service department.
He said an employee had misinterpreted the company's political neutrality policy and the Lego board had not been involved in the decision in October last year.
"It was an internal mistake," Mr Kristiansen said.
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Ai Weiwei is well known for making artworks that criticise the Chinese government and other international political issues, including the European migrant crisis.
When Lego refused to allow the order to make a bulk order for the bricks he instead set up Lego donation points around the world that allowed his fans and supporters to donate bricks for his work instead.
He then used them to make a series of works about free speech and politics.
The bricks were to be used for an art installation in Australia.
Ai told the Lego's decision to no longer question what bulk orders of bricks will be used for was "a victory for freedom of speech".
Lego made the decision to alter their policy in January.
Instead they will ask that customers make it clear that Lego does not endorse any works that use its bricks.
When Lego made the change in January, Ai celebrated by posting a picture to Instagram showing a child stick Lego bricks to his face.
