Tuesday's "attack in Istanbul will play a central role" in the talks, said Steffen Seibert, spokesman for Merkel.
The two leaders will also discuss issues on both countries' priority lists, including their fight against terrorism and a record refugee influx to Europe.
The talks come as part of a regular meeting of the two countries' cabinets, including interior ministers, foreign ministers and defence ministers from both sides.
Turkey has a special relationship with Germany as the biggest EU economy is not only home to around three million people with Turkish roots, but also its biggest trading partner.
It has also stepped up its involvement in the US-led coalition against the Islamic State group, through air strikes as well as the hosting of war planes.