Mr McCrea appeared before the party's disciplinary committee during a three-hour meeting at the UUP headquarters in Belfast.
He was called before the five-strong panel after it was deemed he stepped out of line over comments he made in the media about the ongoing Union Flag dispute.
"The Disciplinary Committee of the Ulster Unionist Party has issued a formal warning to Basil McCrea MLA, following its consideration of two complaints against the Lagan Valley Assembly member," the party said in a statement on Friday.
The UUP stopped short of expulsion or suspension.
"The Committee's decision regarding sanctions was informed by the fact the Party Leader had already withdrawn the Assembly Group Whip from Mr McCrea," the statement added.
The party said the unionist politician was found "guilty of indiscipline and of speaking in a manner that was detrimental to the Party interest" following remarks made during a radio interview.
He was also found guilty "of a public attack on Party policy and consequently of a further act of indiscipline" after separate comments made in a local newspaper and on local radio.
"Mr McCrea has the right of appeal to the Party Officers of the Ulster Unionist Party," the UUP statement added.
Mr McCrea had the UUP whip removed by leader Mike Nesbitt after he said he agreed with the Alliance Party motion of flying the flag on designated days at Belfast City Hall.
He also said he felt his stance was in accordance with UUP policy.
He later opposed his party over a DUP amendment to a UUP motion calling for the Assembly's commitment to inclusivity, mutual respect, peace and democracy, in the wake of the flag unrest.
The DUP wanted to remove a reference to the Good Friday Agreement.
Last week, Mr McCrea said he was happy he was able to have his say during the disciplinary hearing.
"There was an exchange of views, of professional attitude and I had the opportunity to advance my argument," he told UTV.
At the time Mr McCrea maintained he was not considering leaving the party.
However, he didn't rule out legal action if the committee's decision went against him.