There are a few things you need to do to get this working properly.
MSChart accepts DateTime objects as Y values. You can emulate durations by doing this for each of your data points (assuming they are timespans or something convertible into a TimeSpan):
TimeSpan testSpan = TimeSpan.FromMinutes(5);
YourChart.Series(0).Points.AddY(new DateTime(testSpan.Ticks))
That will convert it into a datetime starting from the the beginning of CLR time (e.g. 1/1/0001 12:05:00 AM).
Then just use the label format "HH:mm" on the Y-axis.
<asp:ChartArea Name="VsChartArea">
<AxisY Minimum="0">
<LabelStyle Format="HH:mm" />
</AxisY>
</asp:ChartArea>
That should make it look like this:
To setup a custom interval (5 minutes):
<AxisY Minimum="0" IntervalType="Minutes" Interval="5">
Hope this helps!