I have a table, let\'s call them table SUMMARYDATA
NIP  NAME   DEPARTMENT       STATUSIN           STATUSOUT             TOTALLOSTTIME 
------------         
        use conditional CASE statement in a SUM()
select  DEPARTMENT,
        MONTH(STATUSIN), 
        YEAR(STATUSIN),
        SUM (CASE WHEN TOTALLOSTTIME > '02:00:00') THEN 1 ELSE 0 END) AS RTOTALLOSTTIME 
from    SUMMARYDATA b 
group by DEPARTMENT, MONTH(STATUSIN), YEAR(STATUSIN)
Try the following
select x.department
       ,x.month
       ,x.year     
       ,count(case when x.sum_lost_time >'02:00:00' then NAME end) as RTOTALLOSTTIME 
 from (select MONTH(STATUSIN)  as [month]
               ,YEAR(STATUSIN) as [year]
               ,NIP
               ,NAME
               ,DEPARTMENT         
               ,convert(varchar,dateadd(second,sum(datediff(second,'00:00:00',cast(TOTALLOSTTIME as time))),0),108) as sum_lost_time
          from SUMMARYDATA b 
      group by MONTH(STATUSIN)
               ,YEAR(STATUSIN)
               ,NIP
               ,NAME
               ,DEPARTMENT
        )x
group by  x.department
         ,x.month
         ,x.year        
You are mainly just missing a WHERE clause:
SELECT
    DEPARTMENT,
    MONTH(STATUSIN) AS MONTH,
    YEAR(STATUSIN) AS YEAR,
    SUM(DATEDIFF(second, '00:00:00', TOTALLOSTTIME)) AS sum_lost_time_in_sec
FROM SUMMARYDATA
WHERE
    TOTALLOSTIME > '02:00:00'
GROUP BY
    DEPARTMENT,
    MONTH(STATUSIN),
    YEAR(STATUSIN);