Beqaj is accused of conducting fake procurement procedures in 2022-2023 and issuing fictitious invoices to several companies to divert proceeds to himself and his accomplices in the scheme, SPAK said in a press release.
Beqaj has also failed to declare part of his financial income as a shareholder in a restaurant business.
SPAK said it had started an investigation of the abuse of EU funds in September 2023.
Ilir Beqaj served as health minister from 2013 to 2017 in a government dominated by the Socialist Party. Beqaj headed SASPAC from 2021 to 2023, local media reported.