The Election Commission hit back saying it is not bound to consult the central government before holding any election.
The bypoll yesterday saw large-scale violence resulting in at least eight deaths.
Immediately after the announcement of schedule for the byelections on March 10, the Home Ministry had sent a strongly worded letter to the Commission saying there was no prior consultation with it regarding the bypolls in Srinagar and Anantnag constituencies.
However, the Election Commission ignored the Home Ministry's advice and went ahead, sources in the ministry said today.
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While polling in Srinagar was held on Sunday, byelection in Anantnag will be held on Wednesday.
Later, the Commission sought to reject the claims of the MHA, saying it was its constitutional obligation to hold the bypoll for Srinagar parliamentary constituency before April 16.
"State government was consulted on the subject as it is responsible for law and order and security issues. MHA is only responsible to provide central paramilitary forces. ECI is not bound to consult MHA before holding any elections," an EC source said.
"ECI is responsible for overall assessment of prevailing situation for holding elections. In the assessment of EC, if prevailing conditions were conducive for holding of Panchayat elections by the state government, then holding of parliamentary elections is also possible," the source pointed out.
The EC sources said in the case of Manipur, MHA had wanted to postpone the assembly elections there.
"That too was unsolicited advise. But EC went by its own assessment and held peaceful polls recently. Even the Supreme Court had observed that it is the EC not the MHA who would make assessment of environment of conducting elections," the source said.
Sources in the home ministry said for holding the bypolls in both the constituencies, the Election Commission held a meeting with a Joint Secretary on March 17 and sought 300 companies (30,000 personnel) of paramilitary forces and the request was duly accepted and fulfilled.
The number of paramilitary personnel sought by the EC was very high. But despite presence of a large number of security personnel, the violence yesterday was unusually high, they said.
Normal life has been affected in the Kashmir Valley due to the strike called by separatists. Shops, fuel stations and other business establishments were shut, while attendance in banks and government offices was low.
Internet services remained suspended for the second day today. Public transport was off the roads, while private transport was minimal.