Yes you can. You need to use the @JoinTable and @JoinColumn annotation. Example below:
@Entity
@Table(name = "USER")
public class User {
@Id
@Column(name = "ID")
private Long id;
@ManyToMany
@JoinTable(name = "USER_PERMISSIONS",
joinColumns = @JoinColumn(name = "USER_ID", referencedColumnName = "ID"),
inverseJoinColumns = @JoinColumn(name = "PERM_ID", referencedColumnName = "ID"))
private Collection<Permissions> permissions;
A full working example with bidirectionaly many to many can be found in here http://en.wikibooks.org/wiki/Java_Persistence/ManyToMany