The bill concerns the strategic Golan plateau and east Jerusalem, which Israel occupied in the 1967 Six Day War and later annexed, in moves not recognised by the international community.
Syria has repeatedly demanded a full Israeli withdrawal from the Golan in exchange for peace and the Palestinians want to make east Jerusalem as the capital of their promised state.
Yariv Levin, a supporter of bill and a member of the Likud party, rejected criticism that the bill sought to impede peace.
"It is only appropriate that fateful and significant questions such as the country's borders should be voted by the widest possible majority and not only in Knesset," he told AFP.
The government-backed bill needs to pass two additional readings before becoming a law.
If approved in parliament, the agreement will have to be put to a national referendum within 80 days.