Klotz started work as a contract surveyor of the Dominion government in 1879, and continued in this capacity until 1892 when he became a full-time government employee.  His civil service career lasted forty-four years, until his death in 1923 at the age of seventy-one.

Klotz was active in the Dominion Land Surveys from 1879 to 1884, including the exploratory survey to Hudson Bay which he completed in 1884.  He performed a detailed survey of a river route for a proposed railway, requiring hundreds of astronomical observations, assessing the terrain and its suitability for the proposed project.  His official report and findings determined that the railway and port facilities were practicable but did not believe such a railroad would ever be built.

In 1885, he was assigned by the Dominion Government as chief of the astronomical observations to be conducted in British Columbia and the North West.  This made Klotz the first person in the federal government to be officially designated an astronomer in his job title.  He worked on the British Columbia Railway Belt Survey from 1885 through to 1890, and finally, in the surveys of the Alaska boundary relative to the dispute between the United States and Canada regarding the placement of the boundary during the 1890's.  In the early 1900's Klotz became one of two employees of the Dominion Observatory, the nation's first major astronomical observatory.  In 1916, he became head of that institution when he was appointed Dominion Astronomer.