Under the rules, candidates have to deposit the amount with the returning officer while filing their nomination papers for the post.
A bank official sitting there would count and check the notes, sources said.
Candidates can also deposit the cash at the Reserve Bank of India, enclosing the receipt with the nomination papers.
Sources said candidates were not allowed to make payments digitally or by cheque.
Elected members of the Lok Sabha and the Rajya Sabha and of state legislative assemblies are the electors.
The presidential poll is scheduled to be held on July 17 while the counting of votes is on July 20.