The dispute between the three corporations and the Hyderabad-based Tech Mahindra is likely to hit the citizens as online services will be affected if the company withdraws its technical support.
The company has given a deadline till tomorrow to the municipal corporations to pay the outstanding amount.
The municipal corporations provide various services like RTI, payment of property tax and hawkers' licence, among others, through their e-governance portal.
The MCD on the other hand has accused the company of "pulling its feet away".
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"The company is not correct in telling that around Rs 100 crore is due, as only about Rs 15 crore is outstanding and that too as the company was not able to complete the procedural formalities," South Delhi Municipal Commissioner Manish Gupta told PTI.
The agreement was signed between the two parties in March 2010 when the MCD existed as a single body.
The SDMC Commissioner, however, said that MCD wants to "resolve the issue" and added that the company always had the "option of arbitration".
"We have called a meeting tomorrow where all the three Commissioners will be present and we are looking to resolve this issue soon as we don't want the citizens to suffer," Gupta said.
Sources said that the company has provided services to process as many as 53.4 million transactions worth Rs 1,441 crore in the past three years.