The al-Qaeda-linked group says it has killed more than 50 soldiers and seized military vehicles and weapons.
But a Kenyan military spokesman said the dawn attack was repelled, the base was not overrun and scores of insurgents were killed in the fighting.
A year ago al-Shabab carried out a similar attack on a Kenyan base in the town el-Ade.
In that raid the Islamist group said it had killed more than 100 soldiers, but the Kenyan government refused to give its casualty figures.
