After selling its loss-making handset business, Nokia - which expected the deal to close this month - will derive more than 90 percent of sales from its telecom network unit, but its patent portfolio is seen as a promising source of future growth.
As a phone maker, Nokia has paid rivals for the use of their licences as well as charging for its own. A newly restructured Nokia would be freer to push up those fees, analysts say.
Expected future revenue from patents make up as much as half Nokia's roughly 20-billion-euro market capitalisation, they say.
"(The delay) is a bad sign. They have been discussing with authorities for quite a while already, and they still need more time," Nordea Markets analyst Sami Sarkamies said.
"The biggest risk is in the upside of their patents. It looks like Nokia will have to make bigger concessions to push the deal through," he said.
Nokia shares fell 0.7 percent to 5.24 euros by 1215 GMT.
The Finnish firm said both companies remain committed to the deal, and Microsoft said it expects it to close next month.
"We are nearing the final stages of our global regulatory approval process," Brad Smith, Microsoft's general counsel, said on the company's website. "Currently we are awaiting approval confirmation in the final markets."
Nokia also reiterated that its tax disputes in India would not have an impact on the deal schedule.
Indian authorities hit the company with a new $414 million tax claim last week, following a Supreme Court decision ordering Nokia to give a $571 million guarantee before transferring its Chennai factory to Microsoft.
Pohjola Markets analyst Hannu Rauhala said Nokia and Microsoft had several options on how to deal with the tax issues while the antitrust problem was essentially out of their hands.
"There is always the risk of further postponements (in deal closure). Based on the information they have given today, it can't be ruled out," he said.
The time needed to close the deal, announced last September, is not exceptional for Microsoft, which took five months to complete its purchase of online chat company Skype in 2011. Nokia and Microsoft have already received approvals from the European Commission and the U.S. Department of Justice.
Rauhala said that delays to the deal could also push forward Nokia's strategy update. Nokia had been expected to name a new chief executive and outline its new strategy after the deal.Along with its network unit and patents, future Nokia also includes its navigation software business HERE.