"The Obama administration was under pressure from Hollywood to 'get tough' on copyright enforcement or lose Hollywood's support," Dotcom said in a statement.
"We were the perfect target - successful, high profile, and based outside the United States," he said.
Obama's media team has yet to reply to an emailed request for comment.
In a separate case, Dotcom filed claims for damages of roughly $10 billion in December against US and New Zealand authorities "for the destruction of Megaupload" and the constraints on his liberty for more than seven years.
Dotcom said he filed an application in Auckland, New Zealand's largest city, on Monday asking for Obama to give evidence in his damages claim during his visit to New Zealand.
"There is evidence that President Obama (as he then was) knew the real purpose behind the United States prosecution. That, and further evidence of political motivation in the United States and New Zealand, is set out in the affidavit I have filed in the High Court at Auckland," Dotcom said.
The court has yet to respond to the application and its response could come after Obama's departure.
Obama will be in New Zealand from Wednesday to Friday. He has meetings scheduled with Prime Minister Jacinda Ardern and former prime minister John Key before leaving for Sydney.
Dotcom, who has New Zealand residency, became well known as much for his lavish lifestyle as for his computer skills.
Dozens of black-clad police raided Dotcom's mansion in 2012, breaking him out of a safe room and confiscating millions of dollars in cash and property, including a fleet of luxury cars, computers and art work.
