I need to save two collections in my MongoDB using Java. Where one collection is Department and other collection is Employee. Where one Departm
If $id didn't work try just id like this
"employees" : [ { "$ref" : "employee", "id" : 1 }, { "$ref" : "employee", "id" : 2 } ]
By the provided document and tags I assume you are using spring data to deal with mongodb. So here you may want to use DBRefs to bind employees into departments. Luckily Spring Data gives you @DBRef annotation.
Employee class:
import org.springframework.data.annotation.Id;
import org.springframework.data.mongodb.core.mapping.Document;
@Document
public class Employee {
    @Id
    private Integer id;
    ...
}
Department class:
import org.springframework.data.annotation.Id;
import org.springframework.data.mongodb.core.mapping.DBRef;
import org.springframework.data.mongodb.core.mapping.Document;
@Document
public class Department {
    @Id
    private String id;
    @DBRef
    private Collection<Employee> employees;
    ...
}
MongoDB document:
{
    "_id" : ObjectId("598dc04ac4fdd0e29867ccbb"),
    "_class" : "foo.bar.Department",
    "employees" : [ 
        {
            "$ref" : "employee",
            "$id" : 1
        }, 
        {
            "$ref" : "employee",
            "$id" : 2
        }
    ]
}
Note: Employee instance must already exist in MongoDB. DBRef will not save Employees in cascade style. Look at this article about cascading.