Team Sky are "confident there has been no wrongdoing" after UK Anti-Doping [Ukad] announced it is examining an "allegation" within cycling.
The newspaper alleges a package was delivered to Team Sky in France on June 12, 2011, and it reports that Ukad is looking at what that contained.
Press Association understands Wiggins and his representatives have received no notification from Ukad and believe the 36-year-old is not a subject of the investigation.
And Team Sky insists it is liaising with Ukad after launching an internal review.
A statement from Team Sky read: "Team Sky was contacted by the Daily Mail regarding an allegation of wrongdoing.
"We take any issues such as this very seriously and immediately conducted an internal review to establish the facts. We are confident there has been no wrongdoing.
"We informed British Cycling of the allegation and asked them to contact Ukad, who we will continue to liaise with.
"Team Sky is committed to clean competition. Our position on anti-doping is well known and we 100 per cent stand by that."
Press Association understands the Ukad investigation did not originate from a source within Team Sky or British Cycling.
Ukad, which is dedicated to protecting a culture of clean sport, did not go into any detail about the allegation it is looking at and mentioned no names.
A spokeswoman for Ukad said in a statement: "UK Anti-Doping is investigating an allegation of wrongdoing within cycling. In order to protect the integrity of the investigation, we will not comment further."
According to documents leaked by Russian hacker group Fancy Bears, Wiggins had a therapeutic use exemption (TUE) for triamcinolone acetonide - a synthetic corticosteroid - which was effective from June 29, 2011. Any use of a banned substance requires an active TUE.
The Daily Mail reports that while British Cycling has not identified the substance in the package, it has indicated it did not contain triamcinolone.
Wiggins won the Dauphine Libere stage race - now known as the Criterium du Dauphine - on the day the package was reportedly delivered, completing victory in the eight-day event after the final stage from Pontcharra to La Toussuire.
It was Wiggins' biggest road success to that point of his career and he entered the 2011 Tour as one of the favourites, only to suffer a fractured collarbone on stage seven.
He became the first British winner of the Tour a year later.
It is the latest story which raises questions for Team Sky and team principal Sir Dave Brailsford, the former performance director of British Cycling.
Wiggins and Team Sky have strenuously denied any wrongdoing since it emerged the five-time Olympic champion has received six TUEs during his career, insisting each time the exemptions were medically necessary due to asthma and pollen allergies.
Wiggins used the powerful anti-inflammatory drug triamcinolone - a substance which has a history of abuse in cycling - on the eve of the 2011 and 2012 Tours and 2013 Giro d'Italia.
Wiggins applied, and was granted, three TUEs to take the drug to deal with a pollen allergy that aggravates his long-standing asthma condition.
The TUEs were approved by the UCI, cycling's world governing body, and there is no suggestion that he or the team have broken any rules.
Team Sky have a zero-tolerance policy to doping.
Many riders and staff members have had dual roles with British Cycling and Team Sky squads.
And Jonathan Tiernan-Locke has alleged he was offered a controversial and powerful painkiller while representing Great Britain at the 2012 Road Cycling World Championships.
Tramadol has been on the World Anti-Doping Agency's monitoring list for a number of years, with concerns over its side effects. Some members of the peloton believe its use has contributed to crashes.
Tiernan-Locke told the BBC: "We were offered a painkiller called Tramadol.
"I wasn't in any pain so I didn't need to take it, and that was offered freely around."
Sources within British Cycling say the team doctor at the 2012 Road Cycling World Championships denies the claim.
Tiernan-Locke was the leading British finisher at the race in Limburg, Holland, placing 19th.
Team Sky in 2014 insisted none of their riders used Tramadol after comments from former rider Michael Barry.
Former Team Sky and Endura rider Tiernan-Locke was stripped of the 2012 Tour of Britain title and banned for two years for an anomaly relating to his biological passport. He denies doping.
His Tour of Britain win helped him earn a contract with Team Sky, but he was sacked following his suspension.