Lucy Kabuu, the runner-up at last year's Dubai Marathon, snatched victory in the women's 8km race at the police championships in 27:16.9, ahead of Kiplagat, who timed 27:17.3.
World junior cross country champion Geoffrey Kipsang won the men's 12km race in 35 minutes, while the world's fastest marathon runner Geoffrey Mutai followed in 35:53.7. Kiprop was ninth in 36:53.
Cheruiyot finished outside the top 10 but told reporters she has no interest in the World Cross Country Championships and instead had used the event to prepare for her 5,000m and 10,000m title defences at August's World Athletics Championships in Moscow.
The races are preparing athletes for the national championships next month, when the team for the world championships in Poland in March will be selected.
African double champion Gladys Cherono won the women's 8km at the Defence Forces meeting in Thika, some 45km north of the capital, in 27:40.
Leonard Oleitiptip, who won the race in the last African championships, beat a talent-studded field to take the men's 12km title in 36:07.
Among his casualties was 2010 world cross country champion Joseph Ebuya, who finished fourth in 36:18.
Cherono beat world indoors 3,000m champion Hellen Obiri, 2008 Olympic 1,500m champion Jebet Lagat and former world 10,000m champion Sally Barsosio.