However, Zisling was a noted critic of Ben-Gurion's policies towards Palestinian Arabs, in particular plans to occupy abandoned villages and to destroy standing Arab crops throughout the country after the 1948 Arab-Israeli conflict.
"I couldn’t sleep all night. I felt that things that were going on were hurting my soul, the soul of my family and all of us here (...) Now Jews too have behaved like Nazis and my entire being has been shaken."
In 1949 he was elected to the first Knesset, but Mapam were not included in Ben-Gurion's coalition and Zisling lost his place in the cabinet. He was re-elected in 1951, and was part of the faction that broke away from Mapam to recreate Ahdut HaAvoda. He lost his seat in the 1955 elections and did not return to the Knesset.