"The strong room where the EVMs (Electronic Voting Machines) had been kept in safe custody after the poll process on June 22, was opened in the presence of the contesting candidates and their representatives in Anantnag," an official told IANS.
"The counting process has started and the results should be known before midday."
Eight candidates including Mehbooba Mufti of the Peoples Democratic Party (PDP), Hilal Ahmad Shah of the Congress and Iftikhar Hussain Misgar of the National Conference are contesting.
The constituency has over 84,000 eligible voters and a total of nearly 28,500 voted on Wednesday despite poll boycott called by separatist politicians and militants.
The by-election in Anantnag was necessitated because of the death of the then Chief Minister Mufti Mohammad Sayeed who represented the constituency in the 87-member legislative house.
Sayeed passed away in New Delhi on January 7 after a brief illness.
Mehbooba Mufti assumed power after being sworn in as the Chief Minister of the PDP-BJP coalition government on April 4.
It is mandatory for a Chief Minister or any other minister in the state to become a member of either house of state's bicameral legislature within six months of being sworn in.
At present, Mehbooba Mufti represents the south Kashmir Anantnag Lok Sabha constituency in parliament.