The company will conduct its final flights to those cities over the weekend before suspending all flights from Monday until the end of the month.
“The safety of our passengers and crew members is our top priority at all times,” a spokesperson said.
However, the airline will continue to fly to the city of Lviv in western Ukraine where some countries have moved their embassies.
He added that intelligence shows a conflict between Moscow and Kyiv looks “increasingly likely” at the Munich Security Conference.
Lufthansa follows several other European airlines including Dutch carrier KLM which have already axed services to and from Kyiv.
A spokesperson for Lufthansa said it continued "to monitor the situation closely and is in close contact with national and international authorities".
It added: "Affected guests will be informed and rebooked on alternative flight connections."
On average, the airline operates 74 flights to Ukraine each week under its Lufthansa banner or its other carriers such as Eurowings and Swiss.
Ryanair, the biggest airline to fly between Europe and Ukraine, said last week that it plans to continue to fly to the country.
Ryanair’s chief executive Michael O’Leary said: "It is important not to panic.
"Is it our duty and obligation to support the people of Ukraine as long as there is no war or missiles flying there."
