Criticism over "government-only" flu shots, reserved for soldiers, police officers, and essential workers, comes against the backdrop of a nationwide immunisation campaign due to start next week.
The A/H1N1 virus has so far affected just 23,000 people in Germany, but the government is keen on vaccinating as many people as possible to avoid a possible large-scale outbreak at the start of the winter season.
But revelations in the press that top officials and other essential workers will get the Celvapan vaccine, manufactured by Baxter, which has fewer side effects than the mass Pandemrix vaccine manufactured by GlaxoSmithKline, has caused a public outcry.
Government spokesman Ulrich Wilhelm has rejected accusations of a "two-tier medical system," saying both vaccines have equal worth.
Three vaccines - Pandemrix, Celvapan, and Focetria - have been approved by the European Union to fight the swine flu epidemic and "there isn't a 'better' or a 'worse' one," Wilhelm told a news conference Monday.
Merkel "will be seeing her regular general practitioner, will get his advice, and then will be vaccinated" with Pandemrix, the jab meant for the general public, Wilhelm added.
A number of newspapers nevertheless worried that the government was giving the appearance of double standards.
"How can an ordinary citizen understand that a vaccine with fewer side effects has been ordered for ministers than the one intended for the masses," asked the Frankfurter Allgemeine Zeitung.
Health ministry spokesman Klaus Vater explained that the government had ordered 200,000 vaccines from Baxter last year, in the wake of the bird flu scare, as a precautionary measure to protect essential workers from swine flu.
The government later ordered 50 million vaccines from GlaxoSmithKline to allow for the double dose vaccinations of some 25 million people in Germany, or about a third of the population.
The specialist for health matters at the social-democratic party, Karl Lauterbach, told the Stadt-Anzeiger Cologne newspaper that the Pandemrix jab was not recommended for young children and pregnant women because of possible side effects.
He also strongly criticized the government's information policy saying that the present row might lead people to forgo immunisation altogether.
Recent opinion polls have suggested that Germans are not overly concerned about the flu which appears to have killed only two people to date in the country.
An Emnid poll said 59 percent of Germans had no fear of the flu.
The European Union recently warned against complacency over the spread of swine flu and urged people to get vaccinated even though the virus has not hit as hard as first feared.
"Even if the pandemic situation isn't so dramatic in Europe right now, we have to listen to the experts who say it's not time to lower our guard," said Swedish Public Health Minister Maria Larsson, whose country holds the EU presidency.
The swine flu has killed over 4,700 people in 191 countries and territories since it first appeared in the spring, according to the World Health Organisation.