High Peak Liberal DemocratsThe watchdog said the sum, which is returned if a candidate gets at least 5% of votes cast, was "unreasonable" as it depended on their financial means.
The proposal is one of a series of reforms put forward by the commission to reform the system of deciding who can contest elections in the UK.
Chairwoman Jenny Watson said the current rules were "out of date".
Alongside getting rid of deposits, the commission said the current system of requiring candidates to gather a set number of signatures, which varies depending on the type of election, should be retained.
This process shows a candidate is "genuinely contesting the election", the report said.
The commission said political parties had expressed mixed views about deposits.
Larger parties were mainly in favour, saying the payment deterred "non-serious candidates", its report said.
But smaller parties and independent candidates told the commission the payments could be "unaffordable and therefore they restricted their ability to participate in elections".
The commission concluded: "We do not think that the ability to pay a specified fee is a relevant or appropriate criterion for determining access to the ballot paper."
Deposits are not required in local council elections, while for European Parliament, police and crime commissioner and London Assembly elections, the amount required rises to £5,000.
A £10,000 deposit is required to contest the London mayoral election.
The report also said there was "confusion and inconsistency" in what disqualifies a person from standing for election, and recommended that the requirement to deliver nomination papers in person should be scrapped, with submission by post, email or fax also allowed.
Ms Watson said: "The current rules on standing for election are complex, out of date and difficult for candidates to navigate.
"We've listened to a wide range of views and our recommendations will make it easier for candidates to stand for election in the future, whilst maintaining trust and confidence in the system."
Some of the proposed changes would be complex and require new legislation if adopted by the government, the commission added.
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