Performance drop on INSERT INTO SELECT FROM

We have a "system" with a website. When data is added (never updated old data), we create large "temp_data" table fill it with the new data - couple of million rows, then insert into the "main_data" table: insert into main_data select * from temp_data; main_data is toku_db engine, temp_data is myisam engine. Often during the update, the website stop responding until data is fully inserted: SQLSTATE[HY000] Connection refused and / or SQLSTATE[HY000] MySQL server has gone away Any way I can do the insert "slower". Insert is always new data, it never updates anything.