While Microsoft is spending billions on acquisitions, employees aren't seeing such generosity in their paychecks.

According to an annual companywide survey, obtained by CNBC, Microsoft employees said they're less fairly paid in 2018 than they were in any of the past three years. When asked if "total compensation (base pay, bonus, equity) is competitive compared to similar jobs at other companies," only 61 percent said it was, down from 65 percent in 2017 and 67 percent each of the two prior years.

Additionally, just 62 percent of the employees agreed that "people are rewarded according to their job performance," down from 63 percent last year and 64 percent in 2016. Those two questions received some of the lowest scores on the survey. The company said that 86 percent of Microsoft's employees participated.

The results, shared by Chief People Officer Kathleen Hogan in April, are a further indication of the challenge that Microsoft and other tech companies face in hiring and retaining top talent. Microsoft's headquarters in Redmond, Washington, is just a few miles from Amazon's home and isn't far from the Seattle offices of Google, Facebook and a growing number of start-ups.

As Microsoft continues to expand, through additional hiring and big acquisitions like this week's $7.5 billion GitHub deal, income satisfaction could become a more critical issue inside the company.