Brandon Lewis, the party’s Chairman, has told ITV News those being investigated would not automatically have their voting rights withdrawn, unless they had been suspended or expelled.
He said there was a "long-standing tradition [in this country] that you are innocent until proven guilty".
He told ITV News: "If somebody has posted Islamophobic comments and is found to have done that, we act swiftly, we would not accept them as a member of the party.
"But let's get the difference between the facts and some of the myth... a lot of the cases that people are saying have been referred to the party, and we've looked into them, are not members of the Conservative Party."
His admission comes as we reveal dozens of new allegations of Islamophobic comments, posted online by people who say they are Conservative members.
A dossier of accused individuals we have been compiling since April has now reached almost 200 names.
Among the latest cases, one post describes Islam as a "death cult", another calls Muslims "parasites", while another posted: “Islam = EVIL – FACT".
Another seen by ITV News says: "Islam is an evil death cult that's invaded these shores and it's your God given right to fight it."
The Conservative Party says it acts swiftly to suspend or expel members who post offensive material.
But ITV News has seen emails showing some members are placed under investigation first, during which time they are still eligible to vote in the leadership election.
Speaking in response to our findings, both leadership candidates refused to commit unconditionally to an inquiry into Islamophobia in the party - despite both apparently agreeing to one-time hopeful .
Jeremy Hunt, the current Foreign Secretary, said it was a "good thing" that the party be subject to an "external, independent inquiry" into Islamophobia to ensure it was doing everything it could to root out any cases or people guilty of such behaviour.
But, he added: "The first step is, you have to define what Islamophobia is."
His rival, Boris Johnson, said: "We treat any allegations of prejudice or discrimination or Islamophobia, within our party, any kind of prejudice as absolutely unacceptable.
"We will have an inquiry into every manner of prejudice within the party."
However, Mr Johnson would not commit to a specific inquiry into the claims of Islamophobia, simply saying he was determined to "root out discrimination of any kind".
When asked whether he would be comfortable to get support from someone accused of Islamophobia, Mr Johnson said "absolutely not".
That has now risen to 181 - so 71 new cases are now in the spotlight.
It claimed in a letter to the Equalities and Human Rights Commission there was an “institutional problem” with the Party where racism against Muslims was not being dealt with.
Prominent Tory Baroness Warsi said it was concerning that there appeared to be inconsistencies with how cases were being handled.
"I think if an allegation has been made about Islamophobia or racism, then everybody should be suspended pending an investigation," she said.
"I think it is right that they do not have a say in who becomes leader of the Conservative Party."
In a statement on the latest allegations, the Conservative Party said: “Discrimination or abuse of any kind is wrong and will not be tolerated.
“Where we have been able to identify people the overwhelming majority of these individuals are not members of the Conservative Party and as a result do not have a vote in the leadership contest.
“Any member who is suspended from the party is also not eligible to vote."
In response to the ITV news exclusive, an MCB spokesperson said:"Having first denied any existence of Islamophobia amongst its ranks, we are saddened to see the Conservative Party leadership now obfuscating on the matter.
"At a time of a leadership election, we now hear that it will not be suspending members being investigated of anti-Muslim hatred, whereas in the past it said it would.
"It is truly remarkable that when over well over half its members are found to have conspiratorial views about Muslims propagated by the far-right, the Party continues to deny it has a problem and refuses to take it seriously.
"An external independent inquiry into Islamophobia in the Party is now the absolute minimum needed."