Preheat oven to 180 degrees C. Line two 12 cup muffin tins with paper liners. Sift together the flour, bicarb soda, cocoa powder and salt. Set aside.
In a large bowl, whisk together 1 cup sugar, oil and water until blended. Stir in the vinegar and vanilla. Beat in the flour mixture until incorporated. Set aside.
In a medium bowl, beat together the cream cheese, egg, 1/3 cup sugar and salt. Stir in the chocolate chips.
Fill muffin cups 1/3 full with chocolate batter then top with a heaping tablespoon of the cream cheese mixture. Bake in the preheated oven until the tops spring back when lightly pressed, 20 to 25 minutes.