An alternative way would be to create a new temporary table with same structure.
CREATE TABLE temp_table AS SELECT * FROM original_table LIMIT 0
Then create the primary key in the table.
ALTER TABLE temp_table ADD PRIMARY KEY (primary-key-field)
Finally copy all records from the original table while ignoring the duplicate records.
INSERT IGNORE INTO temp_table AS SELECT * FROM original_table
Now you can delete the original table and rename the new table.
DROP TABLE original_table
RENAME TABLE temp_table TO original_table