The poll panel said that the EVM would lose its originality if changes are made to its internal circuitry.
The Aam Aadmi Party had on Wednesday asked the Election Commission not to have any set guidelines for the EVM challenge as a person planning to hack the machine would not go by the rules set by the poll panel.
The poll watchdog also said the demonstration held inside the Delhi assembly to prove that the machines can be hacked was carried out on a "look alike" EVM and not on the one used by the Election Commission.
"Such so called demonstration on extraneous and duplicate gadgets, which are not owned by the EC cannot be misused and exploited to mislead and influence our intelligent citizens to assail or vilify the EVMS used by the Commission," it told AAP.
Referring to the party's demand to allow it to tamper with the motherboard of the machine, the Election Commission said "allowing any change of the motherboard or any internal circuit of the EVM is like saying that anyone should be permitted to manufacture a new machine and introduce newly made EVMs in EC system, which is implausible and irrational".
The proposed challenge is on June 3 for which seven national and 48 regional parties recognised by the Election Commission have been invited.