"To facilitate taxpayers, late fee on filing of GSTR-3B for August and September has been has been waived," Finance Minister Arun Jaitley tweeted.
He said that the late fee which has been already charged to businesses will be credited back to taxpayers' accounts.
The government had earlier waived late fee for delayed filing of the maiden returns for the month of July under the Goods and Services Tax (GST) regime.
Businesses have been demanding that the government waives penalty for delayed filing of 3B returns.
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As per the data with the GST Network (GSTN), a huge chunk of businesses file their returns after the expiry of the due date.
While only 33.98 lakh July returns were filed till the due date, the number has now gone up to 55.87 lakh. Similarly for August 28.46 lakh returns were filed till the last date, but the figure went up to 51.37 lakh later.
The GST law provides for a nominal fee of Rs 100 per day on Central GST and an equivalent amount on State GST in case of late filing of returns and payment of taxes.