MSD's chief executive Brendan Boyle said this was the going rate for a high-level management and legal programme.
"That kind of international development at a credible programme is going to cost an exceptional amount of money. In many instances here in New Zealand it's the same."
The ministry clarified this morning that the $50,000 bill was included the costs of a two-year post-graduate course, as well as flights and accommodation.
The ministry's spending on PR campaigns rose from $3.4 million to $5.8 million in the last year.
Mr Boyle said he could not immediately say where the increase came from, but it could have been related to the "It's Not Ok" domestic violence campaign.
Spending on contractors rose $3 million in the last financial year to $9.8 million.
MSD bosses said this was mostly as a result of IT investments which were needed to support National's welfare reforms. Mr Boyle said $10 million on contractors was "a pretty small sum" given MSD's $1 billion of spending a year.
Ms Sepuloni responded by saying that the ministry was dealing with "the most cash-strapped" New Zealanders so a $3 million increase should raise eyebrows.
In one case, an EA at the ministry on a two-month contract appeared to have been paid $30,000. The ministry said this incorrect, and the staff member had been employed for five months.
Mr Boyle said MSD was a large organisation which would "always represent some pretty big numbers" and checks on spending were "robust".
Earlier this week, Labour also questioned spending at the Ministry of Business, Innovation and Employment (MBIE) after it was revealed that the department spent $360,000 on furniture when it relocated 200 staff last year, including several $6000 couches.