The apology came only after Kenney faced a barrage of opposition demands to say he's sorry for calling Thomas Lukaszuk "a complete and utter a--hole" in an email to Conservative MPs.
The minister initially wouldn't acknowledge the email. Instead, he repeatedly insisted his government wants to build and maintain ties with the government of Alberta, trying to divert attention away from what was quickly threatening to become a public-relations embarrassment for the Harper government.
"I and this government have a phenomenal, positive working relationship with the government of Alberta," Kenney told the House of Commons amid cackling and jeers from the opposition benches.
"Just yesterday I spent 30 minutes meeting with the provincial finance minister. I've met in the last month with several ministers," Kenney added.
"We have a very strong relationship."
However, a spokesperson for Kenney said the minister later called Lukaszuk to privately offer an apology.
"The Minister spoke with Minister Lukaszuk to apologize for the email message, and to underscore that he looks forward to continuing with the positive working relationship between the Alberta and federal governments," Alexis Pavlich said in a statement.
Kenney's email message was sent last Wednesday as a reply to the office of Tory MP Blaine Calkins, who had asked whether the minister or any of the other 25 Alberta Conservative caucus members would be willing to meet with Lukaszuk.
But Kenney, who represents a Calgary riding, reportedly inadvertently sent the tersely-worded reply not only to Calkins' office, but to all the Alberta Tory caucus and their assistants.
The email then made the rounds of political circles and was seen by some as an example of a souring relationship between the federal and Alberta Tories since the recent Alberta election saw a number of federal Conservatives throw their support behind the province's Wildrose party.
And it put the federal Conservative caucus in an awkward position, with some Tories declining to criticize Kenney while at the same time declaring they have no issues with Lukaszuk.
Asked whether Kenney's comments have poisoned the relationship between the Harper government and Alberta's Conservatives, Tory MP James Rajotte stood behind the minister, but suggested it would be wise for Kenney and others in the Tory caucus to meet with the deputy premier.
"I think it would be a good idea to bring everybody," Rajotte said, noting he will be meeting with Lukaszuk.
But interim Liberal Leader Bob Rae said while the relationship between the two parties isn't great, Kenney went overboard.
"It's obviously a very troubled relationship. I think everybody knows that because of the support by so many people in the Reform cabinet for the Wildrose party," said Rae.
"But that's never an excuse for levelling that kind of an insult."
NDP Leader Tom Mulcair said he found Lukaszuk to be a "real gentleman" when the two met recently, but wondered aloud why Kenney didn't put the matter behind him more quickly.
"When these things happen, you just do the right thing," said Mulcair.
Earlier Tuesday, Kenney told a Calgary-based provincewide radio show that he wouldn't discuss the matter.
"I'm not going to get into private communications," said Kenney.
"As you might well imagine working with people on different issues you sometimes develop views and differences of opinion, but I'm just not going to get into that."
Alberta's opposition Wildrose party urged Premier Alison Redford to re-think her decision last month to make Lukaszuk the deputy premier.
Wildrose house leader Rob Anderson, who has often crossed swords with Lukaszuk on Twitter, said Lukaszuk is known for a debating style that gets personal quickly.
"Let's face it. Thomas has a reputation and you've got to live with that reputation. Sometimes I think he thinks he's an honorary member of the Soprano family. I mean he's just constantly getting very personal," said Anderson.
"He seems to like to take it outside and gets very vicious and personal at times."
In the Twittersphere Lukaszuk is known for a quick draw, dispensing praise and poison in equal measure. In recent Twitter exchanges he refers to some critics as "trolls," tells a dissenter "you're lost in the conversation" and asks a Wildrose spokesman: "Are you always condescending?"
In February, when the Wildrose campaigned against stiffer drunk driving laws as an infringement on personal rights and due process, Lukaszuk tweeted: "When is the Wildrose handing out promotional crack pipes?"
In the legislature Anderson and Lukaszuk have occasionally taken to yelling insults across the floor at one another, ignoring the Speaker.
"It's hard to know why he'd be tasked with such a sensitive role as deputy premier," said Anderson.
"You want somebody who is diplomatic ... and (Redford) probably picked the most undiplomatic one of the bunch."
Requests to speak to Lukaszuk were sent to the premier's office, which had not responded by late Tuesday.
— with files from Dean Bennett in Edmonton