Increase the length of the tube.
The natural frequency of a tube is determined by the speed of sound in the material of the tube and the length of the tube. Increasing the length of the tube will increase the wavelength of the standing waves that can be formed inside the tube, which in turn will increase the natural frequency of the tube. Decreasing the length of the tube will have the opposite effect, decreasing the natural frequency. Making holes in the tube will change the boundary conditions and may affect the natural frequency, but it is not a guaranteed way to increase it. Changing the composition of the tube will change the speed of sound in the material, which may increase or decrease the natural frequency depending on the new material's properties.
I hope this helps :)