As a safeguard, the department intends to implement a retention sum or a bank guarantee as an option for GST-registered companies, he said.
The bank guarantee is at a minimum rate of 30 per cent of the sum claimed by the company, he said.
The department is using several strategies to resolve the issue of GST refunds, Subromaniam said in a statement today.
For refunds below RM50,000, desk audits have been completed with refunds to be made starting from now, he said.
The number of claims for sums under RM50,000 comprised more than 80 per cent of the total claims submitted, he said.
For claims of between RM50,000 and RM100,000, Subromaniam said refunds will be made at the rate of 80 per cent and only a site visit or sample audit will be made with a 20 per cent retention sum imposed.
"The retention sum will be released after the site visit or sample audit, and is expected to be completed within a year," he said.
For claims exceeding RM100,000, refunds will be given at the rate of 70 per cent of the claimed sum and a field audit will be made through risk management with a bank guarantee given at a minimum rate of 30 per cent, he added.
"These companies will only bear a cost of between 0.9 per cent and 1.5 per cent, with the company having the option of replacing the bank guarantee with the retention sum method.
"Under this method, 70 per cent of the total claim amount will be paid to the company while 30 per cent will be retained, to be paid after the site visit or field audit is completed within two months," he said.