The US president has led a purge of diversity programming and called for greater transparency in university admissions.
Trump's tariffs on imports have kicked-in but there is no clarification on rules for transshipment as yet, Reuters said.
Among the 25 banned books is one by Booker Prize winner Arundhati Roy, one of India's most famous living authors.
The plane had taken off from the capital Nairobi's Wilson Airport and was destined for Somaliland.