The Eisenhower administration did not encourage Joseph McCarthy, but they did not really forcefully go against him until he started to weaken himself by overreaching in his drive to "expose" communists in the government.
Eisenhower, personally, had little respect for McCarthy or for his tactics. However, Eisenhower knew that, early in his time in office, he needed the support of people who approved of McCarthy. This meant that Eisenhower could not afford to alienate them by opposing McCarthy openly.
So, Eisenhower's administration pretty much played along with McCarthy, not opposing him in any open way. Later on, though, they did not do anything to defend him as he lost credibility and had his career destroyed by the "Army-McCarthy hearings."