In a memorandum, Antonio Magsanay Jr. of the Commission on Audit (COA) asked Abalos and the commissioners to "take a second look" at their resolution allocating for themselves such "excessive" amounts.
Abalos allowance ran up to P220,000 a month while the commissioners had P100,000 each.
Magsanay said the Comelec resolution violates COA Circular 97-002 which requires that only payments in small amounts may be made through the petty cash fund.
A source said Abalos is also receiving P2.5 million and each commissioner P1.25 million in intelligence funds, which are not subject to auditing.
Comelec Resolution No. 7285, dated July 14 a copy of which was obtained by The STAR shows that the monthly allocation of P100,000 and P220,000 in "petty cash" had been approved by Abalos and the six commissioners.
In justifying the appropriation, the resolution said the offices of the chairman and the commissioners "incur necessary emergency, as well as incidental expenses" in the daily performance of official duties and functions.
"Whereas, in order to facilitate the smooth flow of operations and services of the aforementioned offices, there is a need for the provision of the financial support in the form of operational and miscellaneous expenses," read the resolution.
The resolution requires that all expenses should be certified and all other documents attached to it as a precondition for future "petty cash" disbursements, subject to COA rules and regulations.
However, Magsanays memorandum, dated July 26 a copy of which was also obtained by The STAR pointed out that the petty cash fund is for the whole year, subject to replenishment as frequently as necessary.
It must be supported with receipts, not just a certification, and that the fund (petty cash) must be liquidated at the end of each year.
"Based on the provisions of the aforementioned COA circular, the granting of monthly petty cash fund to the Office of the Chairman and the Commissioners in the amount of P220,000 and P100,000, respectively, appear therefore to be excessive," read the memorandum.
Amid this controversial resolution, Comelec employees have been complaining about delays in the payment of their benefits, and lack of office supplies.
When a power outage hit the Comelec head office in Intramuros, Manila recently, employees were forced to go home as power generators could not be operated due to lack of fuel.
Recently, top Comelec officials met at Clark Field in Pampanga to discuss the future of election modernization.
During the four-day conference, from July 28 to 31, the Comelec reportedly spent some P2 million for food and accommodations at Holiday Inn hotel.
The top officials included all Comelec commissioners down to provincial supervisors, all numbering to about 180.
"It was a package deal," said a source who took part in the conference.
"The hotel rooms were nice, but food was not plenty. Anyway, I think something good came out of the conference. Commissioners would come and go during the four-day event, while one never showed up at all."
The Comelec had already spent P3 billion on the botched 2004 election modernization project after the Supreme Court voided an anomalous contract with a supplier.