Prosecutors said the raids were in connection with the "cum-ex" tax evasion scandal.
German authorities have raided the offices of Morgan Stanley as part of a multi-billion euro tax fraud investigation.
Prosecutors in Cologne confirmed they had searched the Frankfurt branch of the US bank in connection with "cum-ex transactions".
A spokesperson for Morgan Stanley confirmed to Germany's DPA news agency that search warrants had been carried out.
"The investigation relates to past activity and we continue to cooperate with the German authorities," they added.
Around 75 investigators from various authorities in North Rhine-Westphalia and Hesse were involved in the raids, the prosecutor's office said. The private homes of two suspects were also searched for "relevant" communications.
The so-called "cum-ex" scheme consists of quickly buying and selling shares around the dividend payment date so tax authorities can no longer identify the true owner.
The process makes it possible to claim the same tax credit on the profits attached to the dividend several times. According to Germany's finance ministry, the total amount of tax evaded by the company was around €5.5 billion.
Lawyer Hanno Berger has been on trial since April for his role in the alleged tax fraud scheme.