The decision by the charity, which has been working in Afghanistan for over three decades, underlines the growing dangers for aid workers, who have increasingly become casualties of a surge in terrorist violence in recent years.
"We have no choice but to drastically reduce our presence and activities in Afghanistan," Monica Zanarelli, the ICRC head in Afghanistan, told reporters.
"Exposure to risk has become our greater challenge in Afghanistan, and we know that zero risk doesn't exist and we are not aiming at that, but our security has to be guaranteed by every party," she said.
The humanitarian group will close its facilities in the northern city of Maimana, the capital of Faryab province, and in Kunduz province, also in the north and a hotbed of Taliban activity.
Operations in the northern city of Mazar-i-Sharif will be scaled back.
The group has suffered a series of deadly attacks in northern Afghanistan, where Taliban and Islamic State group militants have intensified their assaults on police and troops.
In February six ICRC employees were killed when their convoy came under insurgent attack in the northern province of Jowzjan.
Two of their colleagues were abducted in a separate incident and only released by their captors last month.
No group claimed responsibility for the abduction or killings, but Jowzjan police have blamed local Islamic State jihadists who are making inroads in the country.
Lorena Enebral Perez, 38, was shot inside the aid group's rehabilitation centre in Mazar-i-Sharif, where she treated disabled children, women and men including amputees.
Two people were arrested over the deadly attack, including the 21-year-old shooter whom police said was a "regular patient".
Last December a Spanish Red Cross employee was abducted when workers from the charity were travelling between Mazar-i-Sharif and neighbouring Kunduz. He was released several weeks later.
The ICRC has around 1,800 staff including 120 international aid workers in Afghanistan -- helping wounded and disabled people, supporting hospitals, making prison visits and assisting prisoners to maintain contact with their families.
In many areas such as the north, they are the only international organisation providing such services.
"We understand the consequences to stop our activities in the north but we have no choice," Zanarelli added.
She said the organisation was not leaving Afghanistan but to prevent more losses the "necessity of reviewing our presence is strongly requested".