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One way that I think most organizations would be following is the extensive use of HRIS. I feel now even small organizations would have started using one or the other HRIS technologies for maximum profit.
Zoho, Workday, Peoplesoft are all HRIS that provide login and logout option for the HR to track. They also provide reports with number of hours employees had been logged in. Zoho also allows GPS tracking to ensure login and logout is from the right location.
Apart from this, if you don’t want to spend, emails can be used. Using shared and personalised Google calendar is another method organizations can use. Everyone knows each other’s schedule. Or some kind of calendar along these lines could help.