"We can confirm that Kai Havertz has sustained a hamstring injury during a training session in Dubai last week," Arsenal said in a statement.
"Subsequent assessments and specialist reviews have confirmed that the injury will require surgery, which will take place in the coming days.
"Soon after surgery, Kai will begin his recovery and rehabilitation programme, which is expected to extend into pre-season preparations for next season."
Havertz is Arsenal's top scorer this season with 15 goals in all competitions.
He joins a list of forwards who are out injured, including Gabriel Jesus (anterior cruciate ligament), Bukayo Saka and Gabriel Martinelli (both hamstring).
Saka underwent surgery in late December and is expected to be out of action until March, although the English forward travelled with the squad for the training camp.
Martinelli, meanwhile, limped off in the first half of their EFL Cup semi-final loss at Newcastle United last week, with the Brazilian expected to be sidelined for more than a month.
The injuries leave manager Mikel Arteta with Leandro Trossard, Chelsea loanee Raheem Sterling and academy product Ethan Nwaneri as his options in attack.
The injuries to Martinelli and Havertz occurred less than two weeks after the January transfer window closed, with Arsenal not opting to sign any reinforcements.
Although Arsenal are out of both domestic cups, they are second in the Premier League - six points behind Liverpool - and are also in the last 16 of the Champions League.
Arsenal travel to Leicester City in the league on Saturday.