The Electoral Commission said it had also referred the matter to the police to see if any criminal offences have been committed.
The investigation found that 307 payments totalling £184,676 were missing from the Lib Dems’ spending return without a reasonable excuse.
In addition, invoices supporting 122 out of the 307 payments were missing from the party’s return, the Electoral Commission said.
Bob Posner, director of political finance and regulation at the Electoral Commission, said the case showed why the watchdog should be given powers to impose higher penalties.
He said: “Our investigation uncovered systemic failures in ensuring that the rules were being followed.
“The party and its officers co-operated fully throughout the investigation. However, this is an experienced party that failed to meet the basic requirements of the law, and cases like this undermine voters’ confidence in our political finance system.
“This is why we have applied the highest financial penalty available to us.
“This also highlights why we have been calling on the UK Government to make higher sanctioning powers available to us. With millions of pounds being spent by large parties looking to form national governments, a fine of £20,000 is no longer a strong enough deterrent to ensure the rules are properly followed.”
The Commission has also notified the Metropolitan Police of a possible criminal offence if party officials knowingly or recklessly signed a false declaration in relation to the above spending.
The Liberal Democrats suffered a mauling at the hands of the electorate in 2015, keeping just eight of the 57 seats they had won in 2010.
The investigation concluded that Tim Gordon, the Lib Dems’ registered campaigns officer, committed an offence under the Political Parties, Elections and Referendums Act (PPERA).
The police will now decide whether to investigate if a criminal offence of “knowingly or recklessly making a false declaration” has been committed.
The Commission’s report said: “The evidence provided by the party indicates that some persons within the party were aware of some of the missing payments before the spending return was submitted.
“Consequently some persons within the party were aware that the return was not complete nor correct prior to the campaigns officer signing the accompanying declaration, raising the potential that it was a false declaration.
“The Commission has referred this issue to the Metropolitan Police Service. It will be a matter for the police as to what steps they take following the Commission’s referral.”
A Lib Dem spokesman said: “We always endeavour to ensure our reports of national campaign expenses are completed in full, in good time and according to all applicable rules.
“These mistakes, caused by issues with a small number of local accounting units, were a result of human error and failures of process. We are taking steps to ensure these mistakes are not repeated in future. We will co-operate fully with any investigation.”
Scotland Yard confirmed that officers were looking into the matter.
A spokesman said: “Officers from the special inquiry team are currently assessing an allegation referred to the Met by the Electoral Commission.”