Google, the subject of an EU investigation since November last year, unveiled the Motorola Mobility deal on August 15, its biggest ever, which will see it venturing into video and social networking.
The deal is expected to be notified to regulators on both sides of the Atlantic.
"(The antitrust investigation) is not simple, it is a complex issue," EU Competition Commissioner Joaquin Almunia told Reuters in an interview on the sidelines of the Alpbach Forum Economic Conference.
Asked if the Motorola Mobility deal would affect the antitrust probe, Almunia said: "No, no ... we deal with mergers in a completely separate way than the antitrust cases that we have. Nothing to do (with each other)."
"This is the same company but two different cases, two different procedures, two different analyses, two different teams analyzing but no link."
Almunia also said the Commission may extend the December 13 deadline for deciding whether to clear the planned merger of Deutsche Boerse and NYSE Euronext.
"Regarding the different possibilities of the final deadlines on this in-depth investigation, our decisions should be ready before the yearend or at the beginning of next year. It depends on the different possibilities of using deadlines," he said.
The regulator is now asking the exchanges' rivals whether a combined Deutsche Boerse and NYSE Euronext would block the entry of new players.
Almunia also warned German bank BayernLB that it was running out of time to present a restructuring plan in return for approving the billions of euros it received from the German authorities.
"The fact of the matter is that the Bavarian authorities and the top management of this bank do not seem to fully understand what should be done to get a positive decision regarding the restructuring," he said.
"We see that time is running and more and more people will not be able to understand why BayernLB is not able to present a restructuring plan that can be finally supported with a positive decision."
He also said he was waiting for an overhaul plan from bailed-out Austrian bank Hypo Group Alpe Adria to take into account additional state aid received before the summer.
(Writing by Foo Yun Chee; Editing by Jon Loades-Carter)