Australia needed an unbeaten century from skipper Ricky Ponting to grind out a three-wicket win over Bangladesh in the first test in Fatullah.
''I think the second test is going to be probably harder than the first test,'' Whatmore said in a news conference.
''Because the first test gave them a bit of a scare, they are going to come back very hard. It will be the biggest test for us.'' Bangladesh have won only one of their 43 test matches since 2000, that victory coming over a depleted Zimbabwe side.
The Bangladeshis also lost their first two tests against Australia in 2003 by an innings.
But Bangladesh skipper Habibul Bashar said the first test would have given his team confidence to face Australia in Chittagong tomorrow.
''We will take to the field with more confidence riding on the achievements of the first test,'' Bashar said.
Bashar added that while Australia were undoubtedly flagging after their tour of South Africa, Bangladesh had also had a tough schedule.
''We are also pretty tired playing Sri Lanka and Kenya in February and March,'' he said.