Announcing the latest ban, German health authorities said four batches of the Begripal flu vaccine -- also marketed as Agrippal -- and one batch of the Fluad vaccine were no longer for sale.
Novartis insisted earlier on Thursday that both vaccines were safe despite concerns over impurities.
"Novartis confirms its confidence in the safety and efficacy of its seasonal influenza vaccines," the company said in a statement.
On Wednesday, Italian, Swiss and Austrian authorities stopped sales of the vaccines pending tests into possible side effects.
The alarm was first raised in Italy after white particles were seen in syringes carrying the vaccines, but Novartis stressed that "these particles can occur in the vaccine manufacturing process," adding it was "confident that there is no impact on the safety or efficacy of the vaccine."
The company said it had voluntarily provided Italian health authorities with its assessments "supporting the quality, efficacy and safety" of the vaccines, and that it would continue working with them in a bid to understand their decision to put a freeze on the vaccines.
Shortly after the Italian decision, the Swiss national drug agency Swissmedic also ordered an "immediate halt" of the vaccines owing to "possible impurities".
Their decision was followed by the Austrian health ministry which said on Thursday it had pulled the vaccines because of "possible quality problems" as a "purely a precautionary measure".
"There are currently no indications of any danger to patients," the health ministry said, before recommending alternative medication.
Testing was under way on the vaccines in question, the ministry said, "but this process will take some time," it added.
In Switzerland, where the ban affects some 160,000 vaccine doses, according to Swissmedic, the country risks being unprepared for the winter round of jabs.
Switzerland's Office of Public Health said it had expressly asked pharmaceutical companies to supply flu vaccines but there was still a shortage and the Novartis ban could "aggravate the situation."
Novartis meanwhile stressed that it was "fully committed to providing high quality vaccines to patients and will continue to work with the authorities to make vaccines available."