If you are creating the buttons dynamically, then you can try creating the buttons in a Table cell and then place the table in the panel. This will provide uniform spacing.
I have added a sample HTML to explain the same.
<asp:Panel ID="Panel1" runat="server">
<table>
<tr>
<td><asp:Button ID="Button1" runat="server" Text="Button 1" onclick="Button1_Click" /></td>
<td><asp:Button ID="Button2" runat="server" Text="Button 2" onclick="Button2_Click" /></td>
</tr>
</table>
</asp:Panel>