How measure the voltage over a large resistance?
Two things you can do:


Measure the current flowing through the resistor, then calculate the voltage drop across it (Ohms Law).
Create a Voltage Follower circuit with a much higher input impedance and measure the output voltage of that.


However, by what you're describing, I'm not sure you're using the resistor right in the first place.  Please expand your question with a schematic and a full reasoning behind the use of the resistor.