We report multifrequency phase-referenced observations of the nearby radio galaxy NGC 4261, which has prominent two-sided jets, using the Very Long Baseline Array at 1.4-43 GHz. We measured radio core positions showing observing frequency dependences (known as core shift) in both approaching jets and counter jets. The limit of the core position as the frequency approaches infinity, which suggests a jet base, is separated by 82$pm$16 ${mu}$as upstream in projection, corresponding to (310$pm$60)Rs (Rs: Schwarzschild radius) as a deprojected distance, from the 43 GHz core in the approaching jet. In addition, the innermost component at the counter jet side appeared to approach the same position at infinity of the frequency, indicating that cores on both sides are approaching the same position, suggesting a spatial coincidence with the central engine. Applying a phase referencing technique, we also obtained spectral index maps, which indicate that emission from the counter jet is affected by free-free absorption (FFA). The result of the core shift profile on the counter jet also requires FFA because the core positions at 5-15GHz cannot be explained by a simple core shift model based on synchrotron self-absorption (SSA). Our result is apparently consistent with the SSA core shift with an additional disk-like absorber over the counterjet side. Core shift and opacity profiles at the counter jet side suggest a two-component accretion: a radiatively inefficient accretion flow at the inner region and a truncated thin disk in the outer region. We proposed a possible solution about density and temperature profiles in the outer disk on the basis of the radio observation.