The report comes after Scheuer on Monday questioned Daimler boss Dieter Zetsche in a closed-door meeting over how many Mercedes-Benz vans and cars need to be fixed after a regulator found illegal software in one of its models.
Spiegel, citing no sources, said Scheuer expressed concerns that a total of 750,000 Mercedes vehicles could be affected and that the ministry could impose fines of up to 5,000 euros per car.
A spokesman for the transport ministry said in an email that the carmaker and the transport ministry had agreed to clear up highly complex technical issues related to diesel emissions.
He said concrete steps were agreed following a meeting on Monday in which Transport Minister Andreas Scheuer questioned Zetsche over how many Mercedes vans and cars need to be fixed.
Last month Daimler was ordered by motor vehicle authority KBA to recall Vito vans fitted with 1.6 liter diesel engines because it said they breached emissions rules.
Daimler has said it will appeal against KBA's decision to classify its software as illegal and contest the findings in court if necessary, although it said it was cooperating fully.
Spiegel said there was considerable evidence that diesel engines of the Mercedes C-Class models were also affected and that Daimler representatives would be summoned to the ministry ahead of a planned follow-up meeting of Zetsche and Scheuer later this month.
The report said at least a further 80,000 vehicles might have to be recalled as a result.
A spokesman for Daimler said the group had committed to keeping the nature of its discussions with the Transport Ministry confidential and would not comment.
KBA declined to comment.
Reporting by Madeline Chambers, Holger Hansen, Edward Taylor and Christoph Steitz.