In a statement he went on to attack the CPS and Kent Police for their handling of the case and questioned why the decision had come just days before the election.
The CPS's announcement said Mr Mackinlay, 50, is accused of "falsely" declaring expenses in the run up to the 2015 vote, which saw him narrowly defeat Ukip's Nigel Farage.
But the Conservative said: "My candidature [in 2017] in South Thanet is entirely unaffected and my campaign continues as before.
"I will not let this decision affect the hard work I do for my constituents and the hard work I hope to do for them after the 8th of June."
Allegations were made against a string of Tories after the election two years ago, relating to claims that incorrect expenses were filed for the party’s battle bus tour, but most had been dropped by the CPS up to now, with Mr Mackinlay's the only one outstanding.
The candidate added: "Our justice system is underpinned by the presumption of innocence and I'm confident that I will be acquitted, as I have done nothing wrong and have acted honestly and properly whilst a candidate in 2015, and as all candidates do acted upon advice throughout."
"Clearly this is a shocking decision from the CPS, given that I have done nothing wrong, and I'm confident that this will be made very clear as the matter progresses."
The CPS's investigation saw them question whether any candidates had labelled spending on hotels and campaign material as national spending rather than local, potentially allowing them to increase their constituency campaigning without breaking a legal spending ceiling.
In Mr Mackinlay's case, the focus of the investigation is believed to have centred on whether stays for party workers at the Royal Harbour Hotel in Ramsgate and the Premier Inn in Margate were wrongly attributed to national party expenditure, rather than a local expense.
But the would-be MP went on the offensive, hitting out at prosecutors by saying: "I'm very disappointed with the way this has been handled by the the CPS and Kent Police and I must question the timing of this decision, given that Kent Police confirmed on the 18th of April that their file had been sent to the CPS to review and make their decision.
"Why leave this until a few days before the election?"
Agent Nathan Gray, 28, and Marion Little, 62, have also been charged with offences under the Representation of the People Act 1983 and, with Mr Mackinlay, are due to appear at Westminster Magistrates Court on July 4.
A Conservative Party spokesman said: "We continue to believe that this remaining allegation is unfounded. Our candidate has made clear that there was no intention by him or his campaigners to engage in any inappropriate activity.
"We believe that they have done nothing wrong, and we are confident that this will be proven as the matter progresses. The individuals remain innocent unless otherwise proven guilty in a court of law."
Responding to the news, Labour's leader Jeremy Corbyn said: "Nobody should be commenting on the details of an ongoing case. The police must be allowed to act independently to investigate on the basis of any evidence that they have got.
"The Crown Prosecution Service must be allowed to make it's decision on whether to proceed with the case or not."
The Conservatives have already admitted under-declaring spending on their national 2015 campaign and were fined £70,000 as a result, but they insist all local spending was properly declared. Labour and Liberal Democrats had also been fined by the Electoral Commission in relation to spending returns from 2015.
The Metropolitan Police is also considering whether the treasurer at the time, Simon Day, 'knowingly or recklessly made a false declaration'.
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