Three judges made it 29-28 to Tishchenko, while an Irish judge gave all three rounds to the defending champion.
The decision attracted condemnation from boxing pundits on social media, who suggested it was time for the Hamilton-based Nyika to switch to the professional ranks.
A contentious win isn't new for Tishchenko.
There were angry crowd reactions when he was awarded a unanimous win in the heavyweight gold medal fight at last year's Rio Olympics.
Commonwealth Games light heavyweight champion Nyika opened the tournament with a unanimous points win over German Igor Teziev.
Nyika was the lone Kiwi competing at the AIBA event and hoped to become the second male boxer from his country to claim a world championships medal. The first was David Tua, who took bronze in 1991.NZN dbg/bja