Athletics' world governing body is looking into allegations of "subversion" of the anti-doping process in Kenya and "improper diversion" of funds received from Nike.
Athletics Kenya vice-president David Okeyo and ex-treasurer Joseph Kinyua have also been provisionally suspended.
Their suspensions begin immediately.
The IAAF is also investigating Kiplagat in relation to alleged receipt of an apparent gift of two motor vehicles from the Qatar Association of Athletics Federation in the period 2014-2015.
Okeyo, who is also an IAAF member, was referred to the organisation's ethics commission after being investigated by police in his native country.
He is alleged to have siphoned off funds from a sponsorship deal between the national association and American sportswear firm Nike.
Okeyo has denied any wrongdoing and said all funds had been fully accounted for by Athletics Kenya and audited.
Last week, a group of Kenyan athletes occupied the headquarters of the sport's national governing body, demanding officials resign over corruption allegations.
The IAAF's ethics commission has appointed Sharad Rao - a former director of public prosecutions in Kenya - as its investigator.
Earlier in November, the country had been ordered to explain its doping controls by the World Anti-Doping Agency.
Kenya was one of several countries under scrutiny over how it conducted its testing, with Russia suspended from competition for serious breaches.
And on Saturday, two-time world cross country champion Emily Chebet was named as one of seven athletes to have been suspended by Athletics Kenya for failing drugs tests.
The 2010 and 2013 gold medallist was given a four-year ban after testing positive for the diuretic furosemide.
A total of 43 Kenyan athletes have now been banned for doping and all but three of them have tested positive in the last three years, including Rita Jeptoo, winner of the Boston and Chicago marathons.
President Isaiah Kiplagat and two other Kenya Athletics officials have been provisionally suspended for 180 days by the ethics commission of the IAAF.