The Tories were accused last week of doctoring an interview the shadow Brexit secretary gave to ITV’s Good Morning Britain (GMB).
The video posted by the Conservatives on Twitter made it appear Starmer was unable to answer a question on Brexit.
Speaking to the same programme on Tuesday morning, Sunak admitted it went “a bit too far” and promised the party would learn “lessons”.
“It was done in the spirit of humour but I can appreciate it didn’t land properly,” he said.
“It was a video that was done in jest. I am sorry that it went a bit too far - that’s clearly in hindsight what happened.”
The campaign video posted by the Conservative Party ends with Starmer staring at the camera after being asked by Morgan: “Why would the EU give you a good deal if they know you are going to actively campaign against it?”
However, in the original interview on Tuesday, Sir Keir actually replied to the host: “Well, Piers, I have been talking to the EU, to political leaders across the EU27 countries for three years, and I know very well what the parameters are of any deal that they would do with a Labour government.
“We actually explored some of it in the cross-party talks that we were in with the Government six months or so ago, so I know that a customs union and single market alignment and protection of workers’ rights and environmental rights and consumer rights is something that can be negotiated.”
The edited video has been shared by a number of Conservative parliamentary candidates, including Health Secretary Matt Hancock.
Morgan was among those to criticise the edit. The GMB host tweeted: “Correct, he did [answer the question], albeit not very convincingly – but the way it has been edited is misleading and unfair to Keir Starmer.”
James Cleverly, the chairman of the Conservative Party, has previously defended the video as a “light-hearted satirical video”.