It has also referred one matter, relating to the party's treasurer declaring he had examined the return and believed it to be complete and correct, to the Metropolitan Police.
The investigation found the party's 2015 General Election spending return was missing payments worth at least £104,765.
Separately, payments worth up to £118,124 were either not reported to the Commission or were incorrectly reported.
It said a portion of the amount should have been included in the party's return, while another portion was put into the return when it was candidate spending.
In addition, the Tories did not include invoices or receipts for 81 payments worth £52,924 and failed to maintain records explaining the amounts it invoiced to candidates in three 2014 by-elections for work on their campaigns, meaning the accuracy of the sums could not be verified.
Commission chairman Sir John Holmes said the Tories' failure to follow the rules "undermined voters' confidence in our democratic processes" and said there was a risk political parties were seeing such fines as "a cost of doing business".
The fine comes after a dozen police forces announced they had sent files to the Crown Prosecution Service as part of a probe into the Conservatives' 2015 election expenses.
The allegations centre around whether spending on hotels for visiting activists and certain campaign material was incorrectly registered as national rather than local spending.
At least three Tory MPs have been quizzed by police investigating whether election finance laws were broken in the 2015 contest.
Sir John said: "Our investigation uncovered numerous failures by a large, well-resourced and experienced party to ensure that accurate records of spending were maintained and that all of the party's spending was reported correctly.
"The rules established by Parliament for political parties and their finances are there to ensure transparency and accountability.
"Where the rules are not followed, it undermines voters' confidence in our democratic processes, which is why political parties need to take their responsibilities under the legislation seriously."
He went on: "This is the third investigation we have recently concluded where the largest political parties have failed to report up to six-figure sums following major elections, and have been fined as a result.
"There is a risk that some political parties might come to view the payment of these fines as a cost of doing business; the Commission therefore needs to be able to impose sanctions that are proportionate to the levels of spending now routinely handled by parties and campaigners."
Responding to the investigation, a Conservative Party spokesman said the party had complied fully with the investigation and will pay the fines imposed.
"As we have consistently said, the local agents of Conservative candidates correctly declared all local spending in the 2015 general election."
He said the party's campaign headquarters "accepted in March 2016 that it had made an administrative error by not declaring a small amount constituting 0.6 per cent of our national spending in the 2015 election campaign.
"This error was subsequently corrected and the Party has since improved its accounting practices, reporting structures and staff guidance. Even taking this into account, the Conservative Party still considerably underspent the statutory national spending limits for the 2015 general election."
/The Independent/
More about: #ConservativeParty #electioncampaign #electoralcommission
