The Gunners will be hosting the Championship side four days before they play Bayern at the Emirates Stadium.
German centre-back Mertesacker said Arsenal need to focus and not become complacent to allow Blackburn to cause an FA Cup upset.
"We still have an important cup game on Saturday (first) - we absolutely want to advance in the FA Cup, that is why the preparations for Bayern are not that intense yet," Mertesacker said as part of adidas 'football Hangout on air' webchat.
"However, beginning on Sunday the preparations for Tuesday's match will be extreme.
"Bayern are doing superb this year and that is a big challenge for us, but we are looking forward to both legs."
Bayern Munich have not lost since October 28 and have opened up a 15-point lead at the top of the Bundesliga, maintaining their superb form with four straight wins.
Former Arsenal and Germany goalkeeper Jens Lehmann believes his old club will face a real challenge to progress further in the competition against last season's Champions League finalists who eventually lost out to Chelsea.
Writing in a column for the Sport Bild magazine, Lehmann said: "For an English team it is the worst draw to play a German team directly after the winter break.
"In addition to that Bayern has not been really challenged for once yet in the second half of their season. The only stress they have is the one at the training sessions."
However, Lehmann, 43, believes Arsenal have the quality and players to cause Bayern problems.
He added: "(Bayern coach) Jupp Heynckes will warn his players of the speed that Arsenal still can play in the offensive game, especially Theo Walcott but also more and more Lukas Podolski can be very dangerous.
"Vice-versa, Arsenal will look to stop Bayern creating their good positioning game from which they can accelerate."
Arsenal extended their unbeaten run to five matches with a hard-fought 1-0 Barclays Premier League win against Sunderland.
Gunners boss Arsene Wenger said he was contemplating rotating his squad for the FA Cup tie, in hope of protecting some of his key players.
Captain Thomas Vermaelen missed both the last two matches because of an ankle problem, for which he has been treated with injections.
The Belgian defender said during a Q&A with fans on Arsenal's official Twitter account this morning: "At the moment I feel great, I trained all week, so hopefully I will be back really quickly."
Wenger later revealed Vermaelen was "looking quite good" and could feature this weekend.
However, Wenger said midfielder Jack Wilshere was still be closely monitored after coming off against Sunderland with a dead leg.
Speaking to the club's official website, arsenal.com, Wenger said: "He is having tests today and tomorrow.
"Jack is looking better. He is still a doubt for Saturday. He's got a kick on the thigh."
Wenger also revealed centre-half Laurent Koscielny was unlikely to feature following a calf injury which saw him limp during the warm-up last weekend, after originally picking up the problem while away on international duty with France.
Full-back Carl Jenkinson will be suspended for the match against Blackburn after his red card at Sunderland last week.
With Kieran Gibbs still out with a thigh injury and Andre Santos having joined Brazilian club Gremio on loan, Wenger's defensive options are, at a push, stretched, so Ignasi Miquel, the 20-year-old Spaniard, looks set to be involved again this weekend.
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