A source close to the state government said the centres were being investigated by the internal auditors.
According to a source close to the state government, RM103,000 were allocated to the Wangsa Maju service centre but they were no documents to show how the funds were used.
The source said all funds to the centre had been frozen pending the investigations. The centre had been told to reimburse money that were "unaccounted for," the source added.
As for the Gombak service centre, the source said an allocation of RM35,000 meant for SMUE did not tally with the number of recipients.
When contacted, Dr Tan said he was not present when the auditors came to the centre Friday morning.
"I was not around when that happened, but I was informed by my assistants that they came this morning.
"I have no problem in cooperating because as far as I am concerned, I have not done anything wrong," he said.
Azmin said that none of the auditors came to see him regarding the matter.
"I don't know anything about this. There was no call, nothing. So, I can't comment much," he said.
It was speculated that the investigation was conducted due to the "lack of cooperation" shown by the two service centres to the Merakyatkan Ekonomi Selangor's welfare programme which oversees the SMUE.
"Other service centres have given full cooperation via official requests," said the source.
But some quarters have speculated that the audit probes were linked to "political enemies" of Selangor Mentri Besar Tan Sri Khalid Ibrahim.
It is public knowledge that Khalid and Azmin don't agree on several state policies.
They are also reported to be neck-and-neck in the party's ongoing race for deputy presidency.
Dr Tan, who heads the PKR disciplinary board, recently suspended the memberships of Khalid's aide, Mustapha Mohd Talib and former political secretary Faekah Hussin over the breach of the party's rules and regulations.
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