The directive came soon after yesterday's clash between the GJM and the police in Darjeeling, according to a senior official at the state secretariat.
The decision of the state government to conduct a special audit of the GTA is seen as an attempt to put pressure on the GJM, which sponsored a 12-hour shutdown today and its chief Bimal Gurung challenged Chief Minister Mamata Banerjee to stop the agitation in the hill saying that it was his writ that "runs in the hill".
Chief Minister Mamata Banerjee had ordered the special audit of funds given to the GTA and finance secretary H K Dwivedi had been instructed to carry it out.
"Earlier, there was no specific deadline set for the submission of the audit report but as per the new directive the finance secretary needs to complete the process and submit the report within two weeks' time," the officer said.
It was learnt that the GTA has so far received nearly Rs 900 crore from the state government and over Rs 600 crore from the Centre since 2012.
A six-member team to conduct the special audit of the GTA was scheduled to reach Darjeeling today.
GTA is an autonomous administrative body for the Darjeeling and Kalimpong hills and its term is set to end in July.
"It seems that the state government is trying to bring out the audit report before the GTA goes for elections and thus put pressure on the GJM," the official said.
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