The decision raises the prospect that Sky's near £1bn move to buy 17.9% of ITV, believed to have been masterminded by chief executive James Murdoch, could backfire.
Sky now faces a detailed investigation by the Competition Commission into the effects of the transaction on competition and on the public interest consideration relating to the diversity of media ownership.
Sky's rival Virgin Media, led by major shareholder Richard Branson, called for the government to intervene following the purchase in November, which it interpreted as an attempt to block any chance it had of pursuing its interest in ITV.
Darling intervened in February by asking the Office of Fair Trading and Ofcom for their views on Sky's part-ownership of ITV.
Darling today said: "My decision reflects consideration of the reports I have received from both the Office of Fair Trading and Ofcom and of other representations I have received about this matter. On the basis of the evidence before me, a fuller investigation by the Competition Commission is justified."
The OFT reported to Darling on April 27 that in its opinion the situation had resulted, or may be expected to result, in a substantial lessening of competition within the market.
On the same day Ofcom said it was concerned that the transaction raised public interest issues about the plurality of news provision for both cross-media and television news.
Sky issued the following response to today's decision: "Sky notes today's announcement by the Secretary of State for Trade and Industry. We look forward to engaging with the Competition Commission as the ongoing regulatory process enters its next phase."