Perhaps because of his reluctance to authorise this SADF deployment, Ahtisaari was alleged to have been targeted by the South African Civil Cooperation Bureau (CCB). According to a hearing in September 2000 of the South African Truth and Reconciliation Commission, two CCB operatives (Kobus le Roux and Ferdinand Barnard) were tasked not to kill Ahtisaari, but to give him "a good hiding". To carry out the assault, Barnard had planned to use the grip handle of a metal saw as a knuckleduster. In the event, Ahtisaari did not attend the meeting at the Keetmanshoop Hotel, where Le Roux and Barnard lay in wait for him, and thus Ahtisaari escaped injury.
Often encountering resistance from the Finnish parliament, which preferred a more cautious foreign policy, as well as from within his own party, Ahtisaari did not seek re-election in 2000. He wanted the Social Democrats to re-nominate him for the presidency without opposition, but two opponents signed up for the party's presidential primary. Ahtisaari was the last "strong president", before the 2000 constitution reduced the president's powers. He was succeeded by the foreign minister Tarja Halonen.
Since leaving office, Ahtisaari has held positions in various international organisations. In 2000, he became Chairman of the Brussels-based International Crisis Group, an NGO to which he committed $100,000 in government funding in 1994 one month after becoming elected President of Finland. He remains Chairman Emeritus.
Ahtisaari also founded the independent Crisis Management Initiative (CMI) with the goal of developing and sustaining peace in troubled areas. On 1 December 2000, Ahtisaari was awarded the J. William Fulbright Prize for International Understanding by the Fulbright Association in recognition of his work as peacemaker in some of the world's most troubled areas. In May 2017 Ahtisaari suggested as new CMI leader Alexander Stubb a Finnish politician representing Finnish conservatives i.e. the National Coalition Party.