The vibrational wavepacket of a diatomic molecular ion at the time of ionization is usually considered to be generated on the basis of the Franck-Condon principle. According to this principle, the amplitude of each vibrational wavefunction in the wavepacket is given by the overlap integral between each vibrational wavefunction and the ground vibrational wavefunction in the neutral molecule, and hence, the amplitude should be a real number, or equivalently, a complex number the phase of which is equal to zero. Here we report the observation of a non-trivial phase modulation of the amplitudes of vibrational wavefunctions in a wavepacket generated in the ground electronic state of a H₂⁺ molecular ion at the time of ionization. The phase modulation results in a group delay of the specific vibrational states of order 1 fs, which can be regarded as the settling time required to compose the initial vibrational wavepacket.