Israel had initially approved the entry of 627 Palestinians, of which 413 entered Gaza on Sunday and Monday, before agreeing to allow in another 1,000.
Hamas has criticised the plan, saying it increases Israel's control over Gaza.
Some say the entry process was made easier for supporters of the governing Fatah party of Mahmud Abbas, the Palestinian president, while Hamas members have been refused entry.
The Rafah crossing is operated by Egypt, EU monitors, Israel and the Palestinians, and can be closed if any one party refuses to participate.
The Erez crossing is a long bus ride away from Rafah, where most Palestinians wait to enter Gaza.