In Switzerland (at least in recent times), the Federal Council issues explanatory booklets for matters subject to popular votes (e.g. constitutional amendments and initiatives, referendums against government or parliamentary decisions). In these booklets, the subjects are explained in context and the arguments for "both" sides are presented.
It usually if not always contains the recommendation from the Federal Council and the Parliament (as expected, usually a "no" for initiatives, a "yes" for federal decisions; I should ask a different question on if they've ever supported a popular initiative directly or decided to be against their own decisions).
Has the Federal Council ever taken a different position than the Parliament for any popular votes? Can (as in, would it violate a constitutional principle if) the Federal Council even take a different position in case of a referendum against a law passed by the Parliament?